Merge branch 'lammps:develop' into mliappy_unified

.gitattributes

@@ -3,6 +3,7 @@
 .github export-ignore
 .lgtm.yml export-ignore
 SECURITY.md export-ignore
+CITATION.cff export-ignore
 *       text=auto
 *.jpg   -text
 *.pdf   -text

CITATION.cff

@@ -0,0 +1,91 @@
+# YAML 1.2
+---
+cff-version: 1.2.0
+title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator"
+type: software
+authors:
+  - family-names: "Plimpton"
+    given-names: "Steven J."
+  - family-names: "Kohlmeyer"
+    given-names: "Axel"
+    orcid: "https://orcid.org/0000-0001-6204-6475"
+  - family-names: "Thompson"
+    given-names: "Aidan P."
+    orcid: "https://orcid.org/0000-0002-0324-9114"
+  - family-names: "Moore"
+    given-names: "Stan G."
+  - family-names: "Berger"
+    given-names: "Richard"
+    orcid: "https://orcid.org/0000-0002-3044-8266"
+doi: 10.5281/zenodo.3726416
+license: GPL-2.0-only
+url: https://www.lammps.org
+repository-code: https://github.com/lammps/lammps/
+keywords:
+  - "Molecular Dynamics"
+  - "Materials Modeling"
+message: "If you are referencing LAMMPS in a publication, please cite the paper below."
+preferred-citation:
+  type: article
+  doi: "10.1016/j.cpc.2021.108171"
+  url: "https://www.sciencedirect.com/science/article/pii/S0010465521002836"
+  authors:
+  - family-names: "Thompson"
+    given-names: "Aidan P."
+    orcid: "https://orcid.org/0000-0002-0324-9114"
+  - family-names: "Aktulga"
+    given-names: "H. Metin"
+  - family-names: "Berger"
+    given-names: "Richard"
+    orcid: "https://orcid.org/0000-0002-3044-8266"
+  - family-names: "Bolintineanu"
+    given-names: "Dan S."
+  - family-names: "Brown"
+    given-names: "W. Michael"
+  - family-names: "Crozier"
+    given-names: "Paul S."
+  - family-names: "in 't Veld"
+    given-names: "Pieter J."
+  - family-names: "Kohlmeyer"
+    given-names: "Axel"
+    orcid: "https://orcid.org/0000-0001-6204-6475"
+  - family-names: "Moore"
+    given-names: "Stan G."
+  - family-names: "Nguyen"
+    given-names: "Trung Dac"
+  - family-names: "Shan"
+    given-names: "Ray"
+  - family-names: "Stevens"
+    given-names: "Mark J."
+  - family-names: "Tranchida"
+    given-names: "Julien"
+  - family-names: "Trott"
+    given-names: "Christian"
+  - family-names: "Plimpton"
+    given-names: "Steven J."
+  title: "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales"
+  journal: "Computer Physics Communications"
+  keywords:
+   - Molecular dynamics
+   - Materials modeling
+   - Parallel algorithms
+   - LAMMPS
+  month: 2
+  volume: 271
+  issn: 0010-4655
+  pages: 108171
+  year: 2022
+references:
+ - title: "Fast Parallel Algorithms for Short-Range Molecular Dynamics"
+   type: article
+   journal: Journal of Computational Physics
+   volume: 117
+   number: 1
+   pages: "1-19"
+   year: 1995
+   issn: 0021-9991
+   doi: 10.1006/jcph.1995.1039
+   url: https://www.sciencedirect.com/science/article/pii/S002199918571039X
+   authors:
+   - family-names: "Plimpton"
+     given-names: "Steve"

cmake/CMakeLists.txt

@@ -154,6 +154,19 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
+# set path to python interpreter and thus enforcing python version if
+# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
+  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+  else()
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+  endif()
+  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+  message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
+    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
+endif()
+
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
 mark_as_advanced(LAMMPS_MACHINE)
 if(LAMMPS_MACHINE)
@@ -203,7 +216,7 @@ set(STANDARD_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -404,9 +417,11 @@ endif()
 
 if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
+  if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
-  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+  endif()
+  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
     include(CheckGeneratorSupport)
     if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
       status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
@@ -635,7 +650,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -785,6 +800,10 @@ if(BUILD_SHARED_LIBS)
       set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
     endif()
   else()
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(BUILD_IS_MULTI_CONFIG)
@@ -817,11 +836,17 @@ endif()
 ###############################################################################
 if(BUILD_SHARED_LIBS OR PKG_PYTHON)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
       set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
     endif()
   else()
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(Python_EXECUTABLE)

cmake/Modules/Packages/GPU.cmake

@@ -233,7 +233,8 @@ elseif(GPU_API STREQUAL "OPENCL")
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
-          set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
+          message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
+          "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
       else()
           set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
       endif()
@@ -261,6 +262,8 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
+  elseif(HIP_PLATFORM STREQUAL "spirv")
+    set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
     set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
@@ -340,6 +343,13 @@ elseif(GPU_API STREQUAL "HIP")
           VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
           DEPENDS ${CU_FILE}
           COMMENT "Generating ${CU_NAME}.cubin")
+    elseif(HIP_PLATFORM STREQUAL "spirv")
+      configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
+
+      add_custom_command(OUTPUT ${CUBIN_FILE}
+        VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+        DEPENDS ${CU_CPP_FILE}
+        COMMENT "Gerating ${CU_NAME}.cubin")
       endif()
 
     add_custom_command(OUTPUT ${CUBIN_H_FILE}

cmake/Modules/Packages/LATTE.cmake

@@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE)
   # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
   list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
   list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
-  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
+    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
+                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
   endif()
 
   include(ExternalProject)

cmake/Modules/Packages/MDI.cmake

@@ -26,8 +26,21 @@ if(DOWNLOAD_MDI)
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(NOT PYTHON_VERSION_STRING)
+      set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+      # search for interpreter first, so we have a consistent library
+      find_package(PythonInterp) # Deprecated since version 3.12
+      if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      endif()
+    endif()
+    # search for the library matching the selected interpreter
+    set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
     find_package(PythonLibs QUIET) # Deprecated since version 3.12
     if(PYTHONLIBS_FOUND)
+      if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+        message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+      endif()
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   else()

cmake/Modules/Packages/MISC.cmake

@@ -0,0 +1,13 @@
+# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package
+if(NOT PKG_MC)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
+  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h)
+  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -1,8 +1,28 @@
 if(CMAKE_VERSION VERSION_LESS 3.12)
+  if(NOT PYTHON_VERSION_STRING)
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    # search for interpreter first, so we have a consistent library
+    find_package(PythonInterp) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+  endif()
+  # search for the library matching the selected interpreter
+  set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
   find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
+  if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+    message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+  endif()
   target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
 else()
+  if(NOT Python_INTERPRETER)
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
   find_package(Python REQUIRED COMPONENTS Interpreter Development)
   target_link_libraries(lammps PRIVATE Python::Python)
 endif()

cmake/presets/all_off.cmake

@@ -12,7 +12,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/all_on.cmake

@@ -14,7 +14,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/mingw-cross.cmake

@@ -8,7 +8,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/most.cmake

@@ -10,7 +10,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/windows.cmake

@@ -6,7 +6,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

doc/Makefile

@@ -242,7 +242,6 @@ $(MATHJAX):
 $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
-		(cd utils/converters;\
+		pip install -e utils/converters;\
-		python setup.py develop);\
 		deactivate;\
 	)

doc/src/Build_extras.rst

@@ -123,6 +123,7 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
+   -D HIP_PATH                  # path to HIP installation. Must be set if GPU_API=HIP
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
@@ -179,10 +180,17 @@ set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
+Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
+code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must 
+set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not 
+yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you 
+should only use this option in preparations to run on Aurora system at ANL. 
+
 .. code:: bash
 
    # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
+   export HIP_PATH=/path/to/HIP/install
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
@@ -191,6 +199,7 @@ and the linker to work correctly.
 
    # AMDGPU target (ROCm >= 4.1)
    export HIP_PLATFORM=amd
+   export HIP_PATH=/path/to/HIP/install
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
@@ -199,10 +208,20 @@ and the linker to work correctly.
    # CUDA target (not recommended, use GPU_ARCH=cuda)
    # !!! DO NOT set CMAKE_CXX_COMPILER !!!
    export HIP_PLATFORM=nvcc
+   export HIP_PATH=/path/to/HIP/install
    export CUDA_PATH=/usr/local/cuda
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
    make -j 4
 
+.. code:: bash
+
+   # SPIR-V target (Intel GPUs)
+   export HIP_PLATFORM=spirv
+   export HIP_PATH=/path/to/HIP/install
+   export CMAKE_CXX_COMPILER=<hipcc/clang++>
+   cmake -D PKG_GPU=on -D GPU_API=HIP ..
+   make -j 4
+
 Traditional make
 ^^^^^^^^^^^^^^^^
 
@@ -790,6 +809,8 @@ library.
 
          -D DOWNLOAD_LATTE=value      # download LATTE for build, value = no (default) or yes
          -D LATTE_LIBRARY=path        # LATTE library file (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
 
       If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
       and built inside the CMake build directory.  If the LATTE library
@@ -797,6 +818,13 @@ library.
       ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
       file, not the directory the library file is in.
 
+      The LATTE library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the LATTE build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
    .. tab:: Traditional make
 
       You can download and build the LATTE library manually if you
@@ -1913,14 +1941,25 @@ within CMake will download the non-commercial use version.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
          -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
 
-      CMake will try to download and build the QUIP library from GitHub, if it is not
+      CMake will try to download and build the QUIP library from GitHub,
-      found on the local machine. This requires to have git installed. It will use the same compilers
+      if it is not found on the local machine. This requires to have git
-      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      installed. It will use the same compilers and flags as used for
-      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      compiling LAMMPS.  Currently this is only supported for the GNU
-      and installed QUIP library and CMake cannot find it.
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
 
    .. tab:: Traditional make
 

doc/src/Build_manual.rst

@@ -48,18 +48,15 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<sphinx_>`_ document generator tool.  It also incorporates programmer
+<https://sphinx-doc.org>`_ document generator tool.  It also
-documentation extracted from the LAMMPS C++ sources through the `Doxygen
+incorporates programmer documentation extracted from the LAMMPS C++
-<https://doxygen.nl>`_ program.  Currently the translation to HTML, PDF
+sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
-(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
+the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
-readers) are supported.  For that to work a Python 3 interpreter, the
+and MOBI (for Amazon Kindle readers) are supported.  For that to work a
-``doxygen`` tools and internet access to download additional files and
+Python 3 interpreter, the ``doxygen`` tools and internet access to
-tools are required.  This download is usually only required once or
+download additional files and tools are required.  This download is
-after the documentation folder is returned to a pristine state with
+usually only required once or after the documentation folder is returned
-``make clean-all``.
+to a pristine state with ``make clean-all``.
-
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-.. _sphinx: https://www.sphinx-doc.org
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -252,6 +249,5 @@ manual with ``make spelling``.  This requires `a library called enchant
 positives* (e.g. keywords, names, abbreviations) those can be added to
 the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
 
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-
 .. _lws: https://www.lammps.org
+.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

doc/src/Commands.rst

@@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
    Commands_pair
    Commands_bond
    Commands_kspace
+   Commands_dump
 
 .. toctree::
    :maxdepth: 1

doc/src/Commands_all.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================

doc/src/Commands_bond.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 .. _bond:
 
@@ -93,7 +94,7 @@ OPT.
    * :doc:`harmonic (iko) <angle_harmonic>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`spica (o) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:

doc/src/Commands_compute.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Compute commands
 ================

doc/src/Commands_dump.rst

@@ -0,0 +1,56 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
+
+Dump commands
+=============
+
+An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
+
+.. table_from_list::
+   :columns: 5
+
+   * :doc:`atom <dump>`
+   * :doc:`atom/adios <dump_adios>`
+   * :doc:`atom/gz <dump>`
+   * :doc:`atom/mpiio <dump>`
+   * :doc:`atom/zstd <dump>`
+   * :doc:`cfg <dump>`
+   * :doc:`cfg/gz <dump>`
+   * :doc:`cfg/mpiio <dump>`
+   * :doc:`cfg/uef <dump_cfg_uef>`
+   * :doc:`cfg/zstd <dump>`
+   * :doc:`custom <dump>`
+   * :doc:`custom/adios <dump_adios>`
+   * :doc:`custom/gz <dump>`
+   * :doc:`custom/mpiio <dump>`
+   * :doc:`custom/zstd <dump>`
+   * :doc:`dcd <dump>`
+   * :doc:`deprecated <dump>`
+   * :doc:`h5md <dump_h5md>`
+   * :doc:`image <dump_image>`
+   * :doc:`local <dump>`
+   * :doc:`local/gz <dump>`
+   * :doc:`local/zstd <dump>`
+   * :doc:`molfile <dump_molfile>`
+   * :doc:`movie <dump_image>`
+   * :doc:`netcdf <dump_netcdf>`
+   * :doc:`netcdf/mpiio <dump>`
+   * :doc:`vtk <dump_vtk>`
+   * :doc:`xtc <dump>`
+   * :doc:`xyz <dump>`
+   * :doc:`xyz/gz <dump>`
+   * :doc:`xyz/mpiio <dump>`
+   * :doc:`xyz/zstd <dump>`
+   * :doc:`yaml <dump>`
+

doc/src/Commands_fix.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Fix commands
 ============

doc/src/Commands_kspace.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 KSpace solvers
 ==============

doc/src/Commands_pair.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Pair_style potentials
 ======================
@@ -181,9 +182,9 @@ OPT.
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
-   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/spica (gko) <pair_spica>`
-   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/spica/coul/long (go) <pair_spica>`
-   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/spica/coul/msm (o) <pair_spica>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@@ -270,6 +271,7 @@ OPT.
    * :doc:`spin/magelec <pair_spin_magelec>`
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
+   * :doc:`srp/react <pair_srp>`
    * :doc:`sw (giko) <pair_sw>`
    * :doc:`sw/angle/table <pair_sw_angle_table>`
    * :doc:`sw/mod (o) <pair_sw>`

doc/src/Developer.rst

@@ -17,6 +17,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_updating
    Developer_plugins
    Developer_unittest
    Classes

doc/src/Developer_updating.rst

@@ -0,0 +1,324 @@
+Notes for updating code written for older LAMMPS versions
+---------------------------------------------------------
+
+This section documents how C++ source files that are available *outside
+of the LAMMPS source distribution* (e.g. in external USER packages or as
+source files provided as a supplement to a publication) that are written
+for an older version of LAMMPS and thus need to be updated to be
+compatible with the current version of LAMMPS.  Due to the active
+development of LAMMPS it is likely to always be incomplete.  Please
+contact developer@lammps.org in case you run across an issue that is not
+(yet) listed here.  Please also review the latest information about the
+LAMMPS :doc:`programming style conventions <Modify_style>`, especially
+if you are considering to submit the updated version for inclusion into
+the LAMMPS distribution.
+
+Available topics in mostly chronological order are:
+
+- `Setting flags in the constructor`_
+- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
+- `Use ev_init() to initialize variables derived from eflag and vflag`_
+- `Use utils::numeric() functions instead of force->numeric()`_
+- `Use utils::open_potential() function to open potential files`_
+- `Simplify customized error messages`_
+- `Use of "override" instead of "virtual"`_
+- `Simplified and more compact neighbor list requests`_
+
+----
+
+Setting flags in the constructor
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As LAMMPS gains additional functionality, new flags may need to be set
+in the constructor or a class to signal compatibility with such features.
+Most of the time the defaults are chosen conservatively, but sometimes
+the conservative choice is the uncommon choice, and then those settings
+need to be made when updating code.
+
+Pair styles:
+
+  - ``manybody_flag``: set to 1 if your pair style is not pair-wise additive
+  - ``restartinfo``: set to 0 if your pair style does not store data in restart files
+
+
+Rename of pack/unpack_comm() to pack/unpack_forward_comm()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 8Aug2014
+
+In this change set the functions to pack data into communication buffers
+and to unpack data from communication buffers for :doc:`forward
+communications <Developer_comm_ops>` were renamed from ``pack_comm()``
+and ``unpack_comm()`` to ``pack_forward_comm()`` and
+``unpack_forward_comm()``, respectively.  Also the meaning of the return
+value of these functions was changed: rather than returning the number
+of items per atom stored in the buffer, now the total number of items
+added (or unpacked) needs to be returned.  Here is an example from the
+`PairEAM` class.  Of course the member function declaration in corresponding
+header file needs to be updated accordingly.
+
+Old:
+
+.. code-block:: C++
+
+   int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+   {
+     int m = 0;
+     for (int i = 0; i < n; i++) {
+       int j = list[i];
+       buf[m++] = fp[j];
+     }
+     return 1;
+   }
+
+New:
+
+.. code-block:: C++
+
+   int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+   {
+     int m = 0;
+     for (int i = 0; i < n; i++) {
+       int j = list[i];
+       buf[m++] = fp[j];
+     }
+     return m;
+   }
+
+.. note::
+
+   Because the various "pack" and "unpack" functions are defined in the
+   respective base classes as dummy functions doing nothing, and because
+   of the the name mismatch the custom versions in the derived class
+   will no longer be called, there will be no compilation error when
+   this change is not applied.  Only calculations will suddenly produce
+   incorrect results because the required forward communication calls
+   will cease to function correctly.
+
+Use ev_init() to initialize variables derived from eflag and vflag
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 29Mar2019
+
+There are several variables that need to be initialized based on
+the values of the "eflag" and "vflag" variables and since sometimes
+there are new bits added and new variables need to be set to 1 or 0.
+To make this consistent, across all styles, there is now an inline
+function ``ev_init(eflag, vflag)`` that makes those settings
+consistently and calls either ``ev_setup()`` or ``ev_unset()``.
+Example from a pair style:
+
+Old:
+
+.. code-block:: C++
+
+   if (eflag || vflag) ev_setup(eflag, vflag);
+   else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+New:
+
+.. code-block:: C++
+
+   ev_init(eflag, vflag);
+
+Not applying this change will not cause a compilation error, but
+can lead to inconsistent behavior and incorrect tallying of
+energy or virial.
+
+Use utils::numeric() functions instead of force->numeric()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+The "numeric()" conversion functions (including "inumeric()",
+"bnumeric()", and "tnumeric()") have been moved from the Force class to
+the utils namespace.  Also they take an additional argument that selects
+whether the ``Error::all()`` or ``Error::one()`` function should be
+called in case of an error.  The former should be used when *all* MPI
+processes call the conversion function and the latter *must* be used
+when they are called from only one or a subset of the MPI processes.
+
+Old:
+
+.. code-block:: C++
+
+    val = force->numeric(FLERR, arg[1]);
+    num = force->inumeric(FLERR, arg[2]);
+
+New:
+
+.. code-block:: C++
+
+    val = utils::numeric(FLERR, true, arg[1], lmp);
+    num = utils::inumeric(FLERR, false, arg[2], lmp);
+
+.. seealso::
+
+   :cpp:func:`utils::numeric() <LAMMPS_NS::utils::numeric>`,
+   :cpp:func:`utils::inumeric() <LAMMPS_NS::utils::inumeric>`,
+   :cpp:func:`utils::bnumeric() <LAMMPS_NS::utils::bnumeric>`,
+   :cpp:func:`utils::tnumeric() <LAMMPS_NS::utils::tnumeric>`
+
+Use utils::open_potential() function to open potential files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+The :cpp:func:`utils::open_potential()
+<LAMMPS_NS::utils::open_potential>` function must be used to replace
+calls to ``force->open_potential()`` and should be used to replace
+``fopen()`` for opening potential files for reading.  The custom
+function does three additional steps compared to ``fopen()``: 1) it will
+try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
+error on a units mismatch and will print the date info, if present, in
+the log file; 2) for pair styles that support it, it will set up
+possible automatic unit conversions based on the embedded unit
+information and LAMMPS' current units setting; 3) it will not only try
+to open a potential file at the given path, but will also search in the
+folders listed in the ``LAMMPS_POTENTIALS`` environment variable.  This
+allows to keep potential files in a common location instead of having to
+copy them around for simulations.
+
+Old:
+
+.. code-block:: C++
+
+   fp = force->open_potential(filename);
+   fp = fopen(filename, "r");
+
+New:
+
+.. code-block:: C++
+
+   fp = utils::open_potential(filename, lmp);
+
+Simplify customized error messages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 14May2021
+
+Aided by features of the bundled {fmt} library, error messages now
+can have a variable number of arguments and the string will be interpreted
+as a {fmt} style format string so that custom error messages can be
+easily customized without having to use temporary buffers and ``sprintf()``.
+Example:
+
+Old:
+
+.. code-block:: C++
+
+   if (fptr == NULL) {
+     char str[128];
+     sprintf(str,"Cannot open AEAM potential file %s",filename);
+     error->one(FLERR,str);
+   }
+
+New:
+
+.. code-block:: C++
+
+   if (fptr == nullptr)
+     error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
+
+Use of "override" instead of "virtual"
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 17Feb2022
+
+Since LAMMPS requires C++11 we switched to use the "override" keyword
+instead of "virtual" to indicate polymorphism in derived classes.  This
+allows the C++ compiler to better detect inconsistencies when an
+override is intended or not.  Please note that "override" has to be
+added to **all** polymorph functions in derived classes and "virtual"
+*only* to the function in the base class (or the destructor).  Here is
+an example from the ``FixWallReflect`` class:
+
+Old:
+
+.. code-block:: C++
+
+   FixWallReflect(class LAMMPS *, int, char **);
+   virtual ~FixWallReflect();
+   int setmask();
+   void init();
+   void post_integrate();
+
+New:
+
+.. code-block:: C++
+
+   FixWallReflect(class LAMMPS *, int, char **);
+   ~FixWallReflect() override;
+   int setmask() override;
+   void init() override;
+   void post_integrate() override;
+
+This change set will neither cause a compilation failure, nor will it
+change functionality, but if you plan to submit the updated code for
+inclusion into the LAMMPS distribution, it will be requested for achieve
+a consistent :doc:`programming style <Modify_style>`.
+
+Simplified function names for forward and reverse communication
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 24Mar2022
+
+Rather then using the function name to distinguish between the different
+forward and reverse communication functions for styles, LAMMPS now uses
+the type of the "this" pointer argument.
+
+Old:
+
+.. code-block:: C++
+
+   comm->forward_comm_pair(this);
+   comm->forward_comm_fix(this);
+   comm->forward_comm_compute(this);
+   comm->forward_comm_dump(this);
+   comm->reverse_comm_pair(this);
+   comm->reverse_comm_fix(this);
+   comm->reverse_comm_compute(this);
+   comm->reverse_comm_dump(this);
+
+New:
+
+.. code-block:: C++
+
+   comm->forward_comm(this);
+   comm->reverse_comm(this);
+
+This change is required or else the code will not compile.
+
+Simplified and more compact neighbor list requests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 24Mar2022
+
+This change set reduces the amount of code required to request a
+neighbor list.  It enforces consistency and no longer requires to change
+internal data of the request.  More information on neighbor list
+requests can be :doc:`found here <Developer_notes>`. Example from the
+``ComputeRDF`` class:
+
+Old:
+
+.. code-block:: C++
+
+   int irequest = neighbor->request(this,instance_me);
+   neighbor->requests[irequest]->pair = 0;
+   neighbor->requests[irequest]->compute = 1;
+   neighbor->requests[irequest]->occasional = 1;
+   if (cutflag) {
+     neighbor->requests[irequest]->cut = 1;
+     neighbor->requests[irequest]->cutoff = mycutneigh;
+   }
+
+New:
+
+.. code-block:: C++
+
+   auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
+   if (cutflag) req->set_cutoff(mycutneigh);
+
+Public access to the ``NeighRequest`` class data members has been
+removed so this update is *required* to avoid compilation failure.

doc/src/Errors_messages.rst

@@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Bonds defined but no bond types*
    The data file header lists bonds but no bond types.
 
-*Bond/react: Cannot use fix bond/react with non-molecular systems*
-   Only systems with bonds that can be changed can be used. Atom_style
-   template does not qualify.
-
-*Bond/react: Invalid template atom ID in map file*
-   Atom IDs in molecule templates range from 1 to the number of atoms in the template.
-
-*Bond/react: Rmax cutoff is longer than pairwise cutoff*
-   This is not allowed because bond creation is done using the pairwise
-   neighbor list.
-
-*Bond/react: Molecule template ID for fix bond/react does not exist*
-   A valid molecule template must have been created with the molecule
-   command.
-
-*Bond/react: Reaction templates must contain the same number of atoms*
-   There should be a one-to-one correspondence between atoms in the
-   pre-reacted and post-reacted templates, as specified by the map file.
-
-*Bond/react: Unknown section in map file*
-   Please ensure reaction map files are properly formatted.
-
-*Bond/react: Atom/Bond type affected by reaction too close to template edge*
-   This means an atom which changes type or connectivity during the
-   reaction is too close to an 'edge' atom defined in the map
-   file.  This could cause incorrect assignment of bonds, angle, etc.
-   Generally, this means you must include more atoms in your templates,
-   such that there are at least two atoms between each atom involved in
-   the reaction and an edge atom.
-
-*Bond/react: Fix bond/react needs ghost atoms from farther away*
-   This is because a processor needs to map the entire unreacted
-   molecule template onto simulation atoms it knows about. The
-   comm_modify cutoff command can be used to extend the communication
-   range.
-
-*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
-   Self-explanatory.
-
-*Bond/react: First neighbors of chiral atoms must be of mutually different types*
-   Self-explanatory.
-
-*Bond/react: Chiral atoms must have exactly four first neighbors*
-   Self-explanatory.
-
-*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
-   The coordinates of atoms in the pre-reacted template are used to determine
-   chirality.
-
-*Bond/react special bond generation overflow*
-   The number of special bonds per-atom created by a reaction exceeds the
-   system setting. See the read_data or create_box command for how to
-   specify this value.
-
-*Bond/react topology/atom exceed system topology/atom*
-   The number of bonds, angles etc per-atom created by a reaction exceeds
-   the system setting. See the read_data or create_box command for how to
-   specify this value.
-
 *Both restart files must use % or neither*
    Self-explanatory.
 
@@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Cannot use chosen neighbor list style with lj/gromacs/kk*
    Self-explanatory.
 
-*Cannot use chosen neighbor list style with lj/sdk/kk*
+*Cannot use chosen neighbor list style with lj/spica/kk*
    That style is not supported by Kokkos.
 
 *Cannot use chosen neighbor list style with pair eam/kk*
@@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Cannot use newton pair with lj/gromacs/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
+*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/sdk/gpu pair style*
+*Cannot use newton pair with lj/spica/gpu pair style*
    Self-explanatory.
 
 *Cannot use newton pair with lj96/cut/gpu pair style*
@@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    acquire needed info, The comm_modify cutoff command can be used to
    extend the communication range.
 
+*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
+   Only systems with bonds that can be changed can be used. Atom_style
+   template does not qualify.
+
+*Fix bond/react: Invalid template atom ID in map file*
+   Atom IDs in molecule templates range from 1 to the number of atoms in the template.
+
+*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
+   This is not allowed because bond creation is done using the pairwise
+   neighbor list.
+
+*Fix bond/react: Molecule template ID for fix bond/react does not exist*
+   A valid molecule template must have been created with the molecule
+   command.
+
+*Fix bond/react: Reaction templates must contain the same number of atoms*
+   There should be a one-to-one correspondence between atoms in the
+   pre-reacted and post-reacted templates, as specified by the map file.
+
+*Fix bond/react: Unknown section in map file*
+   Please ensure reaction map files are properly formatted.
+
+*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the map
+   file.  This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
+*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
+   This is because a processor needs to map the entire unreacted
+   molecule template onto simulation atoms it knows about. The
+   comm_modify cutoff command can be used to extend the communication
+   range.
+
+*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
+   Self-explanatory.
+
+*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
+   Self-explanatory.
+
+*Fix bond/react: Chiral atoms must have exactly four first neighbors*
+   Self-explanatory.
+
+*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
+   The coordinates of atoms in the pre-reacted template are used to determine
+   chirality.
+
+*Fix bond/react special bond generation overflow*
+   The number of special bonds per-atom created by a reaction exceeds the
+   system setting. See the read_data or create_box command for how to
+   specify this value.
+
+*Fix bond/react topology/atom exceed system topology/atom*
+   The number of bonds, angles etc per-atom created by a reaction exceeds
+   the system setting. See the read_data or create_box command for how to
+   specify this value.
+
 *Fix bond/swap cannot use dihedral or improper styles*
    These styles cannot be defined when using this fix.
 
@@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed
    This is because the computation of constraint forces within a water
    molecule adds forces to atoms owned by other processors.
 
-*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
+*Pair style lj/spica/coul/long/gpu requires atom attribute q*
    The atom style defined does not have this attribute.
 
 *Pair style nb3b/harmonic requires atom IDs*

doc/src/Errors_warnings.rst

@@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    length, multiplying by the number of bonds in the interaction (e.g. 3
    for a dihedral) and adding a small amount of stretch.
 
-*Bond/react: Atom affected by reaction too close to template edge*
-   This means an atom which changes type or connectivity during the
-   reaction is too close to an 'edge' atom defined in the superimpose
-   file. This could cause incorrect assignment of bonds, angle, etc.
-   Generally, this means you must include more atoms in your templates,
-   such that there are at least two atoms between each atom involved in
-   the reaction and an edge atom.
-
 *Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
    Self-explanatory.
 
@@ -212,6 +204,14 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    about changes they made at the same time step and thus it may result
    in unexpected behavior.
 
+*Fix bond/react: Atom affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the superimpose
+   file. This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
 *Fix bond/swap will ignore defined angles*
    See the page for fix bond/swap for more info on this
    restriction.
@@ -810,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
 
 *Using pair tail corrections with pair_modify compute no*
    The tail corrections will thus not be computed.
-

doc/src/Manual.rst

@@ -110,6 +110,7 @@ Command Reference
    angles
    dihedrals
    impropers
+   dumps
    fix_modify_atc_commands
    Bibliography
 

doc/src/Modify_style.rst

@@ -100,13 +100,14 @@ Documentation (strict)
 
 Contributions that add new styles or commands or augment existing ones
 must include the corresponding new or modified documentation in
-`ReStructuredText format <rst>`_ (.rst files in the ``doc/src/`` folder). The
+`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
-documentation shall be written in American English and the .rst file
+folder). The documentation shall be written in American English and the
-must use only ASCII characters so it can be cleanly translated to PDF
+.rst file must use only ASCII characters so it can be cleanly translated
-files (via `sphinx <sphinx>`_ and PDFLaTeX).  Special characters may be included via
+to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
-embedded math expression typeset in a LaTeX subset.
+Special characters may be included via embedded math expression typeset
+in a LaTeX subset.
 
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
 
 When adding new commands, they need to be integrated into the sphinx
 documentation system, and the corresponding command tables and lists
@@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and
 also a spell check, a check for correct anchors and labels, and a check
 for completeness of references all styles in their corresponding tables
 and lists is run.  In case the spell check reports false positives they
-can be added to the file doc/utils/sphinx-config/false_positives.txt
+can be added to the file ``doc/utils/sphinx-config/false_positives.txt``
 
 Contributions that add or modify the library interface or "public" APIs
 from the C++ code or the Fortran module must include suitable doxygen

doc/src/Packages_details.rst

@@ -36,7 +36,7 @@ page gives those details.
    * :ref:`BPM <PKG-BPM>`
    * :ref:`BROWNIAN <PKG-BROWNIAN>`
    * :ref:`CG-DNA <PKG-CG-DNA>`
-   * :ref:`CG-SDK <PKG-CG-SDK>`
+   * :ref:`CG-SPICA <PKG-CG-SPICA>`
    * :ref:`CLASS2 <PKG-CLASS2>`
    * :ref:`COLLOID <PKG-COLLOID>`
    * :ref:`COLVARS <PKG-COLVARS>`
@@ -384,28 +384,30 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
 
 ----------
 
-.. _PKG-CG-SDK:
+.. _PKG-CG-SPICA:
 
-CG-SDK package
+CG-SPICA package
 ------------------
 
 **Contents:**
 
 Several pair styles and an angle style which implement the
-coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
+coarse-grained SPICA (formerly called SDK) model which enables
-simulation of ionic liquids, electrolytes, lipids and charged amino
+simulation of biological or soft material systems.
-acids.
 
-**Author:** Axel Kohlmeyer (Temple U).
+**Original Author:** Axel Kohlmeyer (Temple U).
+
+**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
 
 **Supporting info:**
 
-* src/CG-SDK: filenames -> commands
+* src/CG-SPICA: filenames -> commands
-* src/CG-SDK/README
+* src/CG-SPICA/README
-* :doc:`pair_style lj/sdk/\* <pair_sdk>`
+* :doc:`pair_style lj/spica/\* <pair_spica>`
-* :doc:`angle_style sdk <angle_sdk>`
+* :doc:`angle_style spica <angle_spica>`
-* examples/PACKAGES/cgsdk
+* examples/PACKAGES/cgspica
 * https://www.lammps.org/pictures.html#cg
+* https://www.spica-ff.org/
 
 ----------
 

doc/src/Packages_list.rst

@@ -78,10 +78,10 @@ whether an extra library is needed to build and use the package:
      - src/CG-DNA/README
      - PACKAGES/cgdna
      - no
-   * - :ref:`CG-SDK <PKG-CG-SDK>`
+   * - :ref:`CG-SPICA <PKG-CG-SPICA>`
-     - SDK coarse-graining model
+     - SPICA (SDK) coarse-graining model
-     - :doc:`pair_style lj/sdk <pair_sdk>`
+     - :doc:`pair_style lj/spica <pair_spica>`
-     - PACKAGES/cgsdk
+     - PACKAGES/cgspica
      - no
    * - :ref:`CLASS2 <PKG-CLASS2>`
      - class 2 force fields

doc/src/angle_spica.rst

@@ -1,32 +1,32 @@
-.. index:: angle_style sdk
+.. index:: angle_style spica
-.. index:: angle_style sdk/omp
+.. index:: angle_style spica/omp
 
-angle_style sdk command
+angle_style spica command
-=======================
+=========================
 
-Accelerator Variants: *sdk/omp*
+Accelerator Variants: *spica/omp*
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   angle_style sdk
+   angle_style spica
 
-   angle_style sdk/omp
+   angle_style spica/omp
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   angle_style sdk
+   angle_style spica
    angle_coeff 1 300.0 107.0
 
 Description
 """""""""""
 
-The *sdk* angle style is a combination of the harmonic angle potential,
+The *spica* angle style is a combination of the harmonic angle potential,
 
 .. math::
 
@@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
 
 where :math:`\theta_0` is the equilibrium value of the angle and
 :math:`K` a prefactor, with the *repulsive* part of the non-bonded
-*lj/sdk* pair style between the atoms 1 and 3.  This angle potential is
+*lj/spica* pair style between the atoms 1 and 3.  This angle potential is
-intended for coarse grained MD simulations with the CMM parameterization
+intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
-using the :doc:`pair_style lj/sdk <pair_sdk>`.  Relative to the
+using the :doc:`pair_style lj/spica <pair_spica>`.  Relative to the
-pair_style *lj/sdk*, however, the energy is shifted by
+pair_style *lj/spica*, however, the energy is shifted by
 :math:`\epsilon`, to avoid sudden jumps.  Note that the usual 1/2 factor
 is included in :math:`K`.
 
@@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
 radians internally; hence :math:`K` is effectively energy per
 radian\^2.
 
-The required *lj/sdk* parameters are extracted automatically from the
+The required *lj/spica* parameters are extracted automatically from the
 pair_style.
 
+Style *sdk*, the original implementation of style *spica*, is available
+for backward compatibility.
+
 ----------
 
 .. include:: accel_styles.rst
@@ -64,14 +67,14 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-CG-SDK package.  See the :doc:`Build package <Build_package>` doc
+CG-SPICA package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
+:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
-:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
+:doc:`pair_style lj/spica/coul/long <pair_spica>`
 
 Default
 """""""

doc/src/angle_style.rst

@@ -92,7 +92,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
-* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
+* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
 * :doc:`table <angle_table>` - tabulated by angle
 
 ----------

doc/src/compute_contact_atom.rst

@@ -8,10 +8,11 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID contact/atom
+   compute ID group-ID contact/atom group2-ID
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * contact/atom = style name of this compute command
+* group2-ID = optional argument to restrict which atoms to consider for contacts (see below)
 
 Examples
 """"""""
@@ -19,6 +20,7 @@ Examples
 .. code-block:: LAMMPS
 
    compute 1 all contact/atom
+   compute 1 all contact/atom mygroup
 
 Description
 """""""""""
@@ -45,6 +47,9 @@ overview of LAMMPS output options.
 The per-atom vector values will be a number >= 0.0, as explained
 above.
 
+The optional *group2-ID* argument allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'.
+
 Restrictions
 """"""""""""
 
@@ -63,4 +68,7 @@ Related commands
 Default
 """""""
 
+*group2-ID* = all
+
+
 none

doc/src/dump.rst

@@ -1,4 +1,26 @@
 .. index:: dump
+.. index:: dump atom
+.. index:: dump cfg
+.. index:: dump custom
+.. index:: dump dcd
+.. index:: dump local
+.. index:: dump xtc
+.. index:: dump yaml
+.. index:: dump xyz
+.. index:: dump atom/gz
+.. index:: dump cfg/gz
+.. index:: dump custom/gz
+.. index:: dump local/gz
+.. index:: dump xyz/gz
+.. index:: dump atom/mpiio
+.. index:: dump cfg/mpiio
+.. index:: dump custom/mpiio
+.. index:: dump xyz/mpiio
+.. index:: dump atom/zstd
+.. index:: dump cfg/zstd
+.. index:: dump custom/zstd
+.. index:: dump xyz/zstd
+.. index:: dump local/zstd
 
 dump command
 ============

doc/src/dump_image.rst

@@ -1,4 +1,5 @@
 .. index:: dump image
+.. index:: dump movie
 
 dump image command
 ==================

doc/src/dump_netcdf.rst

@@ -1,4 +1,5 @@
 .. index:: dump netcdf
+.. index:: dump netcdf/mpiio
 
 dump netcdf command
 ===================

doc/src/dumps.rst

@@ -0,0 +1,8 @@
+Dump Styles
+###############
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   dump*

doc/src/pair_spica.rst

@@ -1,27 +1,27 @@
-.. index:: pair_style lj/sdk
+.. index:: pair_style lj/spica
-.. index:: pair_style lj/sdk/gpu
+.. index:: pair_style lj/spica/gpu
-.. index:: pair_style lj/sdk/kk
+.. index:: pair_style lj/spica/kk
-.. index:: pair_style lj/sdk/omp
+.. index:: pair_style lj/spica/omp
-.. index:: pair_style lj/sdk/coul/long
+.. index:: pair_style lj/spica/coul/long
-.. index:: pair_style lj/sdk/coul/long/gpu
+.. index:: pair_style lj/spica/coul/long/gpu
-.. index:: pair_style lj/sdk/coul/long/omp
+.. index:: pair_style lj/spica/coul/long/omp
-.. index:: pair_style lj/sdk/coul/msm
+.. index:: pair_style lj/spica/coul/msm
-.. index:: pair_style lj/sdk/coul/msm/omp
+.. index:: pair_style lj/spica/coul/msm/omp
 
-pair_style lj/sdk command
+pair_style lj/spica command
-=========================
+===========================
 
-Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp*
+Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp*
 
-pair_style lj/sdk/coul/long command
+pair_style lj/spica/coul/long command
-===================================
+=====================================
 
-Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp*
+Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp*
 
-pair_style lj/sdk/coul/msm command
+pair_style lj/spica/coul/msm command
-==================================
+====================================
 
-Accelerator Variants: *lj/sdk/coul/msm/omp*
+Accelerator Variants: *lj/spica/coul/msm/omp*
 
 Syntax
 """"""
@@ -30,14 +30,14 @@ Syntax
 
    pair_style style args
 
-* style = *lj/sdk* or *lj/sdk/coul/long*
+* style = *lj/spica* or *lj/spica/coul/long*
 * args = list of arguments for a particular style
 
 .. parsed-literal::
 
-     *lj/sdk* args = cutoff
+     *lj/spica* args = cutoff
        cutoff = global cutoff for Lennard Jones interactions (distance units)
-     *lj/sdk/coul/long* args = cutoff (cutoff2)
+     *lj/spica/coul/long* args = cutoff (cutoff2)
        cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
        cutoff2 = global cutoff for Coulombic (optional) (distance units)
 
@@ -46,21 +46,21 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style lj/sdk 2.5
+   pair_style lj/spica 2.5
    pair_coeff 1 1 lj12_6 1 1.1 2.8
 
-   pair_style lj/sdk/coul/long 10.0
+   pair_style lj/spica/coul/long 10.0
-   pair_style lj/sdk/coul/long 10.0 12.0
+   pair_style lj/spica/coul/long 10.0 12.0
    pair_coeff 1 1 lj9_6 100.0 3.5 12.0
 
-   pair_style lj/sdk/coul/msm 10.0
+   pair_style lj/spica/coul/msm 10.0
-   pair_style lj/sdk/coul/msm 10.0 12.0
+   pair_style lj/spica/coul/msm 10.0 12.0
    pair_coeff 1 1 lj9_6 100.0 3.5 12.0
 
 Description
 """""""""""
 
-The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
+The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential,
 given by
 
 .. math::
@@ -71,14 +71,20 @@ given by
    E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
                          \left(\frac{\sigma}{r}\right)^4 \right]
                          \qquad r < r_c \\
+   E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon
+                         \left[ \left(\frac{\sigma}{r}\right)^{12} -
+                         \left(\frac{\sigma}{r}\right)^5 \right]
+                         \qquad r < r_c \\
    E = &  4 \epsilon  \left[ \left(\frac{\sigma}{r}\right)^{12} -
                          \left(\frac{\sigma}{r}\right)^6 \right]
                          \qquad r < r_c
 
-as required for the SDK Coarse-grained MD parameterization discussed in
+as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
-:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`.  Rc is the cutoff.
+:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
+Rc is the cutoff.
+Summary information on these force fields can be found at https://www.spica-ff.org
 
-Style *lj/sdk/coul/long* computes the adds Coulombic interactions
+Style *lj/spica/coul/long* computes the adds Coulombic interactions
 with an additional damping factor applied so it can be used in
 conjunction with the :doc:`kspace_style <kspace_style>` command and
 its *ewald* or *pppm* or *pppm/cg* option.  The Coulombic cutoff
@@ -92,7 +98,7 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands, or by mixing as described below:
 
-* cg_type (lj9_6, lj12_4, or lj12_6)
+* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6)
 * epsilon (energy units)
 * sigma (distance units)
 * cutoff1 (distance units)
@@ -108,11 +114,15 @@ and Coulombic interactions for this type pair.  If both coefficients
 are specified, they are used as the LJ and Coulombic cutoffs for this
 type pair.
 
-For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
+For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be
 specified since a Coulombic cutoff cannot be specified for an
 individual I,J type pair.  All type pairs use the same global
 Coulombic cutoff specified in the pair_style command.
 
+The original implementation of the above styles are
+style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*,
+and available for backward compatibility.
+
 ----------
 
 .. include:: accel_styles.rst
@@ -123,24 +133,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
+and cutoff distance for all of the lj/spica pair styles *cannot* be mixed,
 since different pairs may have different exponents. So all parameters
 for all pairs have to be specified explicitly through the "pair_coeff"
 command. Defining then in a data file is also not supported, due to
 limitations of that file format.
 
-All of the lj/sdk pair styles support the
+All of the lj/spica pair styles support the
 :doc:`pair_modify <pair_modify>` shift option for the energy of the
 Lennard-Jones portion of the pair interaction.
 
-The *lj/sdk/coul/long* pair styles support the
+The *lj/spica/coul/long* pair styles support the
 :doc:`pair_modify <pair_modify>` table option since they can tabulate
 the short-range portion of the long-range Coulombic interaction.
 
-All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
+All of the lj/spica pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
 not need to be specified in an input script that reads a restart file.
 
-The lj/sdk and lj/cut/coul/long pair styles do not support
+The lj/spica and lj/cut/coul/long pair styles do not support
 the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command.
 
 ----------
@@ -148,8 +158,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re
 Restrictions
 """"""""""""
 
-All of the lj/sdk pair styles are part of the CG-SDK package.  The
+All of the lj/spica pair styles are part of the CG-SPICA package.  The
-*lj/sdk/coul/long* style also requires the KSPACE package to be built
+*lj/spica/coul/long* style also requires the KSPACE package to be built
 (which is enabled by default).  They are only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
@@ -157,7 +167,7 @@ doc page for more info.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style spica <angle_spica>`
 
 Default
 """""""
@@ -168,8 +178,16 @@ none
 
 .. _Shinoda3:
 
-**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
+**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007).
 
 .. _DeVane:
 
 **(DeVane)**  Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
+
+.. _Seo:
+
+**(Seo)**  Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
+
+.. _Miyazaki:
+
+**(Miyazaki)**  Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).

doc/src/pair_srp.rst

@@ -1,18 +1,23 @@
 .. index:: pair_style srp
+.. index:: pair_style srp/react
 
 pair_style srp command
 ======================
 
+pair_style srp/react command
+============================
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    pair_style srp cutoff btype dist keyword value ...
+   pair_style srp/react cutoff btype dist react-id keyword value ...
 
 * cutoff = global cutoff for SRP interactions (distance units)
 * btype = bond type to apply SRP interactions to (can be wildcard, see below)
 * distance = *min* or *mid*
+* react-id = id of either fix bond/break or fix bond/create
 * zero or more keyword/value pairs may be appended
 * keyword = *exclude*
 
@@ -36,13 +41,19 @@ Examples
    pair_coeff 1 2 none
    pair_coeff 2 2 srp 40.0
 
+   fix        create all bond/create   100  1  2  1.0 1 prob  0.2  19852
+   pair_style hybrid dpd 1.0 1.0 12345 srp/react 0.8 * min create exclude yes
+   pair_coeff 1 1 dpd 60.0 50 1.0
+   pair_coeff 1 2 none
+   pair_coeff 2 2 srp/react 40.0
+
    pair_style hybrid srp 0.8 2 mid
    pair_coeff 1 1 none
    pair_coeff 1 2 none
    pair_coeff 2 2 srp 100.0 0.8
 
 Description
-"""""""""""
+
 
 Style *srp* computes a soft segmental repulsive potential (SRP) that
 acts between pairs of bonds. This potential is useful for preventing
@@ -121,6 +132,18 @@ at the cutoff distance :math:`r_c`.
 
 ----------
 
+Pair style *srp/react* interfaces the pair style *srp* with the
+bond breaking and formation mechanisms provided by fix *bond/break*
+and fix *bond/create*, respectively. When using this pair style, whenever a
+bond breaking (or formation) reaction occurs, the corresponding fictitious
+particle is deleted (or inserted) during the same simulation time step as
+the reaction. This is useful in the simulation of reactive systems involving
+large polymeric molecules :ref:`(Palkar) <Palkar>`  where the segmental repulsive
+potential is necessary to minimize topological violations, and also needs to be
+turned on and off according to the progress of the reaction.
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -178,3 +201,8 @@ The default keyword value is exclude = yes.
 
 **(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
 Chem Phys, 136 (13) 134903, 2012.
+
+.. _Palkar:
+
+**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
+

doc/src/pair_style.rst

@@ -260,9 +260,9 @@ accelerated styles exist.
 * :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
 * :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
 * :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
-* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
+* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
-* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
+* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
-* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM
+* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
 * :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
 * :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
 * :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
@@ -349,6 +349,7 @@ accelerated styles exist.
 * :doc:`spin/magelec <pair_spin_magelec>` -
 * :doc:`spin/neel <pair_spin_neel>` -
 * :doc:`srp <pair_srp>` -
+* :doc:`srp/react <pair_srp>` -
 * :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
 * :doc:`sw/angle/table <pair_sw_angle_table>` - Stillinger-Weber potential with tabulated angular term
 * :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential

doc/src/variable.rst

@@ -685,7 +685,9 @@ of a run, according to this formula:
 The run begins on startstep and ends on stopstep.  Startstep and
 stopstep can span multiple runs, using the *start* and *stop* keywords
 of the :doc:`run <run>` command.  See the :doc:`run <run>` command for
-details of how to do this.
+details of how to do this.  If called in between runs or during a
+:doc:`run 0 <run>` command, the ramp(x,y) function will return the
+value of x.
 
 The stagger(x,y) function uses the current timestep to generate a new
 timestep.  X,y > 0 and x > y are required.  The generated timesteps
@@ -781,10 +783,14 @@ according to this formula:
 where dt = the timestep size.
 
 The run begins on startstep.  Startstep can span multiple runs, using
-the *start* keyword of the :doc:`run <run>` command.  See the
+the *start* keyword of the :doc:`run <run>` command.  See the :doc:`run
-:doc:`run <run>` command for details of how to do this.  Note that the
+<run>` command for details of how to do this.  Note that the
-:doc:`thermo_style <thermo_style>` keyword elaplong =
+:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
-timestep-startstep.
+If used between runs this function will return
+the value according to the end of the last run or the value of x if
+used before *any* runs.  This function assumes the length of the time
+step does not change and thus may not be used in combination with
+:doc:`fix dt/reset <fix_dt_reset>`.
 
 The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
 x = value0, y = amplitude, z = period.  They use the elapsed time to
@@ -799,10 +805,14 @@ run, according to one of these formulas, where omega = 2 PI / period:
 where dt = the timestep size.
 
 The run begins on startstep.  Startstep can span multiple runs, using
-the *start* keyword of the :doc:`run <run>` command.  See the
+the *start* keyword of the :doc:`run <run>` command.  See the :doc:`run
-:doc:`run <run>` command for details of how to do this.  Note that the
+<run>` command for details of how to do this.  Note that the
-:doc:`thermo_style <thermo_style>` keyword elaplong =
+:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
-timestep-startstep.
+If used between runs these functions will return
+the value according to the end of the last run or the value of x if
+used before *any* runs.  These functions assume the length of the time
+step does not change and thus may not be used in combination with
+:doc:`fix dt/reset <fix_dt_reset>`.
 
 ----------
 

doc/utils/check-styles.py

@@ -60,7 +60,7 @@ reader = {}
 region = {}
 total = 0
 
-index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$")
+index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
 style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
 upper = re.compile("[A-Z]+")
 gpu = re.compile("(.+)/gpu$")
@@ -84,7 +84,8 @@ def load_index_entries_in_file(path):
 
 def load_index_entries():
     index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
-             'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()}
+             'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
+             'kspace_style': set(), 'dump': set()}
     rst_files = glob(os.path.join(doc_dir, '*.rst'))
     for f in rst_files:
         for command_type, style in load_index_entries_in_file(f):
@@ -254,8 +255,9 @@ for command_type, entries in index.items():
 
 print("Total number of style index entries:", total_index)
 
+skip_angle = ('sdk')
 skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
-skip_pair = ('meam/c','lj/sf','reax/c')
+skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
 skip_compute = ('pressure/cylinder')
 
 counter = 0
@@ -269,13 +271,14 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair
 counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
 counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',skip=skip_angle,suffix=True)
-counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
+counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',skip=skip_angle,suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
 counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
 counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
 counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
+counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) <dump.*>`",dump,'Dump',suffix=True)
 
 if counter:
     print(f"Found {counter} issue(s) with style lists")
@@ -284,12 +287,13 @@ counter = 0
 
 counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
 counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
-counter += check_style_index("angle_style", angle, index["angle_style"])
+counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
 counter += check_style_index("bond_style", bond, index["bond_style"])
 counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
 counter += check_style_index("improper_style", improper, index["improper_style"])
 counter += check_style_index("kspace_style", kspace, index["kspace_style"])
-counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
+counter += check_style_index("dump", dump, index["dump"])
+counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
 
 if counter:
     print(f"Found {counter} issue(s) with style index")

doc/utils/sphinx-config/false_positives.txt

@@ -291,6 +291,7 @@ blocksize
 blueviolet
 bn
 bni
+bnumeric
 bo
 Bochkarev
 Bochum
@@ -423,6 +424,8 @@ CGDNA
 cgs
 cgsdk
 CGSDK
+cgspica
+CGSPICA
 Chaimovich
 Chalopin
 Champaign
@@ -1480,6 +1483,7 @@ intra
 intralayer
 intramolecular
 ints
+inumeric
 inv
 invariants
 inversed
@@ -1697,6 +1701,7 @@ kTln
 ktypeN
 Kub
 Kubo
+Kuksenok
 Kumagai
 Kumar
 Kurebayashi
@@ -2086,6 +2091,7 @@ Mishin
 Mishra
 mistyped
 mistyrose
+Miyazaki
 Mj
 mK
 mkdir
@@ -2486,6 +2492,7 @@ ohenrich
 ok
 Okabe
 Okamoto
+Okazaki
 O'Keefe
 OKeefe
 oldlace
@@ -2701,6 +2708,7 @@ polydispersity
 polyelectrolyte
 polyhedra
 Polym
+polymorph
 polymorphism
 Ponder
 popen
@@ -2753,6 +2761,7 @@ pscrozi
 pseudodynamics
 pseudopotential
 pSp
+pSPICA
 Pstart
 Pstop
 pstyle
@@ -3115,6 +3124,7 @@ semiaxes
 semimetals
 Semin
 Sensable
+Seo
 Sep
 seqdep
 Serpico
@@ -3226,6 +3236,8 @@ Spellmeyer
 Speybroeck
 sph
 SPH
+spica
+SPICA
 Spickermann
 splined
 spparks
@@ -3454,6 +3466,7 @@ tmin
 Tmin
 tmp
 tN
+tnumeric
 Tobias
 Toennies
 Tohoku
@@ -3733,6 +3746,7 @@ wallstyle
 walltime
 Waltham
 Waroquier
+Wataru
 wavepacket
 wB
 Wbody

examples/PACKAGES/cgspica/README

@@ -1,7 +1,8 @@
-LAMMPS CG-SDK example problems
+LAMMPS CG-SPICA example problems
 
-Each of these sub-directories contains a sample problem for the SDK
+Each of these sub-directories contains a sample problem for 
-coarse grained MD potentials that you can run with LAMMPS.
+the SPICA (formerly called SDK) coarse grained MD potentials 
+that you can run with LAMMPS.
 
 These are the two sample systems
 
@@ -9,11 +10,11 @@ peg-verlet:	coarse grained PEG surfactant/water mixture lamella
 		verlet version
 		this example uses the plain LJ term only, no charges.
 		two variants are provided regular harmonic angles and
-		the SDK variant that includes 1-3 LJ repulsion.
+		the SPICA variant that includes 1-3 LJ repulsion.
 
 sds-monolayer:  coarse grained SDS surfactant monolayers at water/vapor
 		interface.
-		this example uses the SDK LJ term with coulomb and shows
+		this example uses the SPICA LJ term with coulomb and shows
 		how to use the combined coulomb style vs. hybrid/overlay
 		with possible optimizations due to the small number of
 		charged particles in this system

examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8

@@ -9,7 +9,7 @@ atom_style	angle
 processors * * 1
 
 # read topology and force field
-pair_style	lj/sdk 15.0
+pair_style	lj/sdk 15.0 # compatible with "lj/spica"
 bond_style	harmonic
 angle_style	harmonic
 special_bonds	lj/coul 0.0 0.0 1.0

examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle

@@ -9,9 +9,9 @@ atom_style	angle
 processors * * 1
 
 # read topology and force field
-pair_style	lj/sdk 15.0
+pair_style	lj/sdk 15.0 # compatible with "lj/spica"
 bond_style	harmonic
-angle_style	sdk
+angle_style	sdk # compatible with "spica"
 special_bonds	lj/coul 0.0 0.0 1.0
 
 read_data	data.pegc12e8.gz

examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid

@@ -5,9 +5,9 @@ dimension       3
 atom_style      full
 processors  * * 1
 
-pair_style hybrid/overlay  lj/sdk 15.0  coul/long 26.5
+pair_style hybrid/overlay  lj/sdk 15.0  coul/long 26.5 # "lj/sdk" is compatible with "lj/spica"
 bond_style      harmonic
-angle_style     sdk
+angle_style     sdk # compatible with "spica"
 special_bonds   lj/coul 0.0 0.0 1.0
 
 read_data       data.sds.gz

examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular

@@ -5,9 +5,9 @@ dimension       3
 atom_style      full
 processors  * * 1
 
-pair_style lj/sdk/coul/long 15.0
+pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
 bond_style      harmonic
-angle_style     sdk
+angle_style     sdk # compatible with "spica"
 special_bonds   lj/coul 0.0 0.0 1.0
 
 read_data       data.sds.gz

examples/PACKAGES/srp_react/README

@@ -0,0 +1,16 @@
+This directory contains an input script for performing 
+simulations with the srp/react pair style. The pair style
+srp/react interfaces fix bond/break and fix bond/create commands
+with the segmental repulsive potential. This is useful in simulating 
+reactions with soft potentials such as DPD where minimizing 
+topological violations is important.
+
+The input script in.srp_react is an example of a simulation of
+a degrading nanogel particle. An initial equilibrated structure
+of a nanogel particle (prior to degradation) is read from the 
+restart file. The degradation reaction is simulated via 
+the fix bond/break command. The simulation will generate the 
+file bonds_broken.txt containing the number of bonds 
+broken and fraction of bonds intact over the simulation time. 
+For more details see the LAMMPS online documentation and the 
+paper: Palkar, V., & Kuksenok, O. (2022). JPC B, 126, 336.

examples/PACKAGES/srp_react/in.srp_react

@@ -0,0 +1,95 @@
+## srp_react example script
+## Author: Vaibhav Palkar
+##
+## Simulates controlled degradation of a nanogel particle 
+## in a simulation box and prints statistics regarding
+## the fraction of bonds broken over time.
+
+variable       rseeddpd  equal  26817
+variable       rseedvel  equal  5991
+variable       breakstep equal  10
+variable       probbreak  equal 0.0009
+variable       rseedbreak equal 6777
+
+# simulation time 
+#***********************************************
+variable       mainsteps     equal  10000
+
+# simulation setup
+#***********************************************
+units          lj
+atom_style     molecular
+boundary       p  p  p
+bond_style     harmonic
+#lattice        fcc   3.0
+comm_modify    cutoff 4.0 vel yes
+
+# initial nanogel
+#***********************************************
+read_data   gel_equil.dat
+
+# define groups, create solvent atoms 
+#**************************************************
+group          Npoly         type   1 2 3 4
+group          water         type   5
+group          N_all         type   1 2 3 4 5
+
+# density check
+#***********************************************
+variable       N_atoms  equal  count(all)
+variable       tdens equal count(all)/vol
+print          "The system density is now ${tdens}"
+
+# bond break settings
+# #***********************************************
+fix            break  N_all     bond/break  ${breakstep}   2   0  prob   ${probbreak}    ${rseedbreak}
+
+# interaction parameter setting
+#***********************************************
+mass             *   1.0
+bond_coeff       *   500.0   0.70
+special_bonds  lj   1  1  1
+newton         on
+
+pair_style     hybrid dpd  1.0  1.0  ${rseeddpd} srp/react 0.8 * mid break
+#***********************************************
+pair_coeff     *5     *5   dpd   78.000    4.5   1.0
+pair_coeff     *4      5   dpd   79.500    4.5   1.0
+pair_coeff     *5      6   none
+pair_coeff      6      6   srp/react   80.00 0.800
+
+# initial velocity
+#***********************************************
+velocity       all create 1.0 ${rseedvel} dist gaussian mom yes
+
+# integrator control
+#***********************************************
+neighbor       0.3 bin
+neigh_modify   every 1 delay 5 check  no
+timestep       0.02
+
+# Access variables of fix bond/break
+#**********************************************
+variable      Nbreak    equal  f_break[2]   # Number of bonds broken
+variable      TIME      equal  time
+
+# ensemble setting
+#***********************************************
+fix            1  all  nve
+
+# print bonds breaking stats
+# ***********************************************
+variable TotBreak equal 100 # total breakable bonds in current system
+fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact"
+
+# thermo output
+#***********************************************
+thermo         100
+thermo_style   custom step temp pe ke etotal epair
+thermo_modify  flush  yes  norm  no
+
+reset_timestep 0
+#dump          1 Npoly   custom 5000 traj.lammpstrj id type x y z
+#*********************************************
+run           ${mainsteps}
+#***********************************************

lib/gpu/Makefile.hip

@@ -1,6 +1,9 @@
 # /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for HIP
-#     - export HIP_PLATFORM=amd (or nvcc) before execution
+#     - export HIP_PATH=/path/to/HIP/install path to the HIP implementation
+#       such as hipamd or CHIP-SPV.
+#     - export HIP_PLATFORM=<amd/nvcc/spirv> specify the HIP platform to use.
+#       Optional. If not set, will be determined by ${HIP_PATH}/bin/hipconfig.
 #     - change HIP_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 
@@ -20,9 +23,21 @@ HIP_OPTS = -O3
 HIP_HOST_OPTS = -Wno-deprecated-declarations -fopenmp
 HIP_HOST_INCLUDE =
 
+ifndef HIP_PATH
+$(error HIP_PATH is not set)
+endif
+
+ifndef HIP_PLATFORM
+	HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
+endif
+HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
+
 # use device sort
 # requires linking with hipcc and hipCUB + (rocPRIM or CUB for AMD or Nvidia respectively)
+ifneq (spirv,$(HIP_PLATFORM))
+# hipCUB not aviable for CHIP-SPV
 HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT
+endif
 # path to cub
 HIP_HOST_INCLUDE += -I./
 # path to hipcub
@@ -36,12 +51,19 @@ endif
 # use mpi
 HIP_HOST_OPTS += -DMPI_GERYON -DUCL_NO_EXIT
 # this settings should match LAMMPS Makefile
-MPI_COMP_OPTS = $(shell mpicxx --showme:compile)
+# automatic flag detection for OpenMPI
+ifeq ($(shell mpicxx --showme:compile >/dev/null 2>&1; echo $$?), 0)
+MPI_COMP_OPTS = $(shell mpicxx --showme:compile) -DOMPI_SKIP_MPICXX=1
 MPI_LINK_OPTS = $(shell mpicxx --showme:link)
-
+# automatic flag detection for MPICH
-HIP_PATH ?= $(wildcard /opt/rocm/hip)
+else ifeq ($(shell mpicxx -compile_info >/dev/null 2>&1; echo $$?),0)
-HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
+MPI_COMP_OPTS = $(filter -I%,$(shell mpicxx -compile_info)) -DMPICH_IGNORE_CXX_SEEK
-HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
+MPI_LINK_OPTS = $(filter -Wl%,$(shell mpicxx -link_info)) $(filter -L%,$(shell mpicxx -link_info)) $(filter -l%,$(shell mpicxx -link_info))
+# for other MPI libs: must set flags manually, if needed
+else
+MPI_COMP_OPTS =
+MPI_LINK_OPTS =
+endif
 
 ifeq (hcc,$(HIP_PLATFORM))
 # possible values: gfx803,gfx900,gfx906
@@ -55,6 +77,8 @@ else ifeq (nvcc,$(HIP_PLATFORM))
 		    -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] -gencode arch=compute_53,code=[sm_53,compute_53]\
 			-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] -gencode arch=compute_62,code=[sm_62,compute_62]\
 			-gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_72,code=[sm_72,compute_72] -gencode arch=compute_75,code=[sm_75,compute_75]
+else ifeq (spirv,$(HIP_PLATFORM))
+HIP_ARCH = spirv
 endif
 
 BIN_DIR = .
@@ -71,7 +95,15 @@ BSH = /bin/sh
 HIP_OPTS += -DUSE_HIP $(HIP_PRECISION)
 HIP_GPU_OPTS += $(HIP_OPTS) -I./
 
-ifeq (clang,$(HIP_COMPILER))
+ifeq (spirv,$(HIP_PLATFORM))
+	HIP_HOST_OPTS += -fPIC
+	HIP_GPU_CC  = $(HIP_PATH)/bin/hipcc -c
+	HIP_GPU_OPTS_S = 
+	HIP_GPU_OPTS_E =
+	HIP_KERNEL_SUFFIX = .cpp
+	HIP_LIBS_TARGET = 
+	export HCC_AMDGPU_TARGET := $(HIP_ARCH)
+else ifeq (clang,$(HIP_COMPILER))
 	HIP_HOST_OPTS += -fPIC
 	HIP_GPU_CC  = $(HIP_PATH)/bin/hipcc --genco
 	HIP_GPU_OPTS_S = --offload-arch=$(HIP_ARCH)

lib/gpu/lal_lj_spica.cpp

@@ -1,9 +1,9 @@
 /***************************************************************************
-                                 lj_sdk.cpp
+                                 lj_spica.cpp
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Class for acceleration of the lj/sdk/cut pair style
+  Class for acceleration of the lj/spica/cut pair style
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -14,14 +14,14 @@
  ***************************************************************************/
 
 #if defined(USE_OPENCL)
-#include "lj_sdk_cl.h"
+#include "lj_spica_cl.h"
 #elif defined(USE_CUDART)
-const char *lj_sdk=0;
+const char *lj_spica=0;
 #else
-#include "lj_sdk_cubin.h"
+#include "lj_spica_cubin.h"
 #endif
 
-#include "lal_lj_sdk.h"
+#include "lal_lj_spica.h"
 #include <cassert>
 namespace LAMMPS_AL {
 #define CGCMMT CGCMM<numtyp, acctyp>
@@ -53,33 +53,33 @@ int CGCMMT::init(const int ntypes, double **host_cutsq,
                           const double gpu_split, FILE *_screen) {
   int success;
   success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
-                            _screen,lj_sdk,"k_lj_sdk");
+                            _screen,lj_spica,"k_lj_spica");
   if (success!=0)
     return success;
 
   // If atom type constants fit in shared memory use fast kernel
-  int sdk_types=ntypes;
+  int spica_types=ntypes;
   shared_types=false;
   int max_shared_types=this->device->max_shared_types();
-  if (sdk_types<=max_shared_types && this->_block_size>=max_shared_types) {
+  if (spica_types<=max_shared_types && this->_block_size>=max_shared_types) {
-    sdk_types=max_shared_types;
+    spica_types=max_shared_types;
     shared_types=true;
   }
-  _sdk_types=sdk_types;
+  _spica_types=spica_types;
 
   // Allocate a host write buffer for data initialization
-  UCL_H_Vec<numtyp> host_write(sdk_types*sdk_types*32,*(this->ucl_device),
+  UCL_H_Vec<numtyp> host_write(spica_types*spica_types*32,*(this->ucl_device),
                                UCL_WRITE_ONLY);
 
-  for (int i=0; i<sdk_types*sdk_types; i++)
+  for (int i=0; i<spica_types*spica_types; i++)
     host_write[i]=0.0;
 
-  lj1.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
+  lj1.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY);
-  this->atom->type_pack4(ntypes,sdk_types,lj1,host_write,host_cutsq,
+  this->atom->type_pack4(ntypes,spica_types,lj1,host_write,host_cutsq,
                          host_cg_type,host_lj1,host_lj2);
 
-  lj3.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
+  lj3.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY);
-  this->atom->type_pack4(ntypes,sdk_types,lj3,host_write,host_lj3,host_lj4,
+  this->atom->type_pack4(ntypes,spica_types,lj3,host_write,host_lj3,host_lj4,
                          host_offset);
 
   UCL_H_Vec<double> dview;
@@ -132,7 +132,7 @@ int CGCMMT::loop(const int eflag, const int vflag) {
   } else {
     this->k_pair.set_size(GX,BX);
     this->k_pair.run(&this->atom->x, &lj1, &lj3,
-                     &_sdk_types, &sp_lj, &this->nbor->dev_nbor,
+                     &_spica_types, &sp_lj, &this->nbor->dev_nbor,
                      &this->_nbor_data->begin(), &this->ans->force,
                      &this->ans->engv, &eflag, &vflag, &ainum,
                      &nbor_pitch, &this->_threads_per_atom);

lib/gpu/lal_lj_spica.cu

@@ -1,9 +1,9 @@
 // **************************************************************************
-//                                  lj_sdk.cu
+//                                  lj_spica.cu
 //                             -------------------
 //                           W. Michael Brown (ORNL)
 //
-//  Device code for acceleration of the lj/sdk pair style
+//  Device code for acceleration of the lj/spica pair style
 //
 // __________________________________________________________________________
 //    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -24,7 +24,7 @@ _texture_2d( pos_tex,int4);
 #define pos_tex x_
 #endif
 
-__kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
+__kernel void k_lj_spica(const __global numtyp4 *restrict x_,
                        const __global numtyp4 *restrict lj1,
                        const __global numtyp4 *restrict lj3,
                        const int lj_types,
@@ -91,6 +91,9 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
         } else if (lj1[mtype].y == 1) {
           inv2=r2inv*ucl_sqrt(r2inv);
           inv1=inv2*inv2;
+        } else if (lj1[mtype].y == 4) {
+          inv1=r2inv*r2inv*ucl_sqrt(r2inv);
+          inv2=inv1*r2inv;
         } else {
           inv1=r2inv*r2inv*r2inv;
           inv2=inv1;
@@ -119,7 +122,7 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
                 ans,engv);
 }
 
-__kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_,
+__kernel void k_lj_spica_fast(const __global numtyp4 *restrict x_,
                             const __global numtyp4 *restrict lj1_in,
                             const __global numtyp4 *restrict lj3_in,
                             const __global numtyp *restrict sp_lj_in,
@@ -192,6 +195,9 @@ __kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_,
         } else if (lj1[mtype].y == (numtyp)1) {
           inv2=r2inv*ucl_sqrt(r2inv);
           inv1=inv2*inv2;
+        } else if (lj1[mtype].y == (numtyp)4) {
+          inv1=r2inv*r2inv*ucl_sqrt(r2inv);
+          inv2=inv1*r2inv;
         } else {
           inv1=r2inv*r2inv*r2inv;
           inv2=inv1;

lib/gpu/lal_lj_spica.h

@@ -1,9 +1,9 @@
 /***************************************************************************
-                                  lj_sdk.h
+                                  lj_spica.h
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Class for acceleration of the lj/sdk pair style
+  Class for acceleration of the lj/spica pair style
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -67,7 +67,7 @@ class CGCMM : public BaseAtomic<numtyp, acctyp> {
   bool shared_types;
 
   /// Number of atom types
-  int _sdk_types;
+  int _spica_types;
 
  private:
   bool _allocated;

lib/gpu/lal_lj_spica_ext.cpp

@@ -1,9 +1,9 @@
 /***************************************************************************
-                                  lj_sdk.h
+                                  lj_spica.h
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Functions for LAMMPS access to lj/sdk pair acceleration routines
+  Functions for LAMMPS access to lj/spica pair acceleration routines
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -17,7 +17,7 @@
 #include <cassert>
 #include <cmath>
 
-#include "lal_lj_sdk.h"
+#include "lal_lj_spica.h"
 
 using namespace std;
 using namespace LAMMPS_AL;
@@ -27,7 +27,7 @@ static CGCMM<PRECISION,ACC_PRECISION> CMMMF;
 // ---------------------------------------------------------------------------
 // Allocate memory on host and device and copy constants to device
 // ---------------------------------------------------------------------------
-int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
+int spica_gpu_init(const int ntypes, double **cutsq, int **cg_types,
                  double **host_lj1, double **host_lj2, double **host_lj3,
                  double **host_lj4, double **offset, double *special_lj,
                  const int inum, const int nall, const int max_nbors,
@@ -42,7 +42,7 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
   int gpu_rank=CMMMF.device->gpu_rank();
   int procs_per_gpu=CMMMF.device->procs_per_gpu();
 
-  CMMMF.device->init_message(screen,"lj/sdk",first_gpu,last_gpu);
+  CMMMF.device->init_message(screen,"lj/spica",first_gpu,last_gpu);
 
   bool message=false;
   if (CMMMF.device->replica_me()==0 && screen)
@@ -89,11 +89,11 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
   return init_ok;
 }
 
-void sdk_gpu_clear() {
+void spica_gpu_clear() {
   CMMMF.clear();
 }
 
-int** sdk_gpu_compute_n(const int ago, const int inum_full,
+int** spica_gpu_compute_n(const int ago, const int inum_full,
                         const int nall, double **host_x, int *host_type,
                         double *sublo, double *subhi, tagint *tag, int **nspecial,
                         tagint **special, const bool eflag, const bool vflag,
@@ -105,7 +105,7 @@ int** sdk_gpu_compute_n(const int ago, const int inum_full,
                        vatom, host_start, ilist, jnum, cpu_time, success);
 }
 
-void sdk_gpu_compute(const int ago, const int inum_full, const int nall,
+void spica_gpu_compute(const int ago, const int inum_full, const int nall,
                      double **host_x, int *host_type, int *ilist, int *numj,
                      int **firstneigh, const bool eflag, const bool vflag,
                      const bool eatom, const bool vatom, int &host_start,
@@ -114,7 +114,7 @@ void sdk_gpu_compute(const int ago, const int inum_full, const int nall,
                 firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
 }
 
-double sdk_gpu_bytes() {
+double spica_gpu_bytes() {
   return CMMMF.host_memory_usage();
 }
 

lib/gpu/lal_lj_spica_long.cpp

@@ -1,9 +1,9 @@
 /***************************************************************************
-                               lj_sdk_long.cpp
+                               lj_spica_long.cpp
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Class for acceleration of the lj/sdk/coul/long pair style
+  Class for acceleration of the lj/spica/coul/long pair style
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -14,14 +14,14 @@
  ***************************************************************************/
 
 #if defined(USE_OPENCL)
-#include "lj_sdk_long_cl.h"
+#include "lj_spica_long_cl.h"
 #elif defined(USE_CUDART)
-const char *lj_sdk_long=0;
+const char *lj_spica_long=0;
 #else
-#include "lj_sdk_long_cubin.h"
+#include "lj_spica_long_cubin.h"
 #endif
 
-#include "lal_lj_sdk_long.h"
+#include "lal_lj_spica_long.h"
 #include <cassert>
 namespace LAMMPS_AL {
 #define CGCMMLongT CGCMMLong<numtyp, acctyp>
@@ -58,7 +58,7 @@ int CGCMMLongT::init(const int ntypes, double **host_cutsq,
                            const double g_ewald) {
   int success;
   success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
-                            _screen,lj_sdk_long,"k_lj_sdk_long");
+                            _screen,lj_spica_long,"k_lj_spica_long");
   if (success!=0)
     return success;
 

lib/gpu/lal_lj_spica_long.cu

@@ -1,9 +1,9 @@
 // **************************************************************************
-//                                lj_sdk_long.cu
+//                                lj_spica_long.cu
 //                             -------------------
 //                           W. Michael Brown (ORNL)
 //
-//  Device code for acceleration of the lj/sdk/coul/long pair style
+//  Device code for acceleration of the lj/spica/coul/long pair style
 //
 // __________________________________________________________________________
 //    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -29,7 +29,7 @@ _texture( q_tex,int2);
 #define q_tex q_
 #endif
 
-__kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
+__kernel void k_lj_spica_long(const __global numtyp4 *restrict x_,
                             const __global numtyp4 *restrict lj1,
                             const __global numtyp4 *restrict lj3,
                             const int lj_types,
@@ -107,6 +107,9 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
           } else if (lj3[mtype].x == (numtyp)1) {
             inv2=r2inv*ucl_rsqrt(rsq);
             inv1=inv2*inv2;
+          } else if (lj3[mtype].x == (numtyp)4) {
+            inv1=r2inv*r2inv*ucl_rsqrt(rsq);
+            inv2=inv1*r2inv;
           } else {
             inv1=r2inv*r2inv*r2inv;
             inv2=inv1;
@@ -157,7 +160,7 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
                   vflag,ans,engv);
 }
 
-__kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_,
+__kernel void k_lj_spica_long_fast(const __global numtyp4 *restrict x_,
                                  const __global numtyp4 *restrict lj1_in,
                                  const __global numtyp4 *restrict lj3_in,
                                  const __global numtyp *restrict sp_lj_in,
@@ -236,6 +239,9 @@ __kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_,
           } else if (lj3[mtype].x == (numtyp)1) {
             inv2=r2inv*ucl_rsqrt(rsq);
             inv1=inv2*inv2;
+          } else if (lj3[mtype].x == (numtyp)4) {
+            inv1=r2inv*r2inv*ucl_rsqrt(rsq);
+            inv2=inv1*r2inv;
           } else {
             inv1=r2inv*r2inv*r2inv;
             inv2=inv1;

lib/gpu/lal_lj_spica_long.h

@@ -1,9 +1,9 @@
 /***************************************************************************
-                                lj_sdk_long.h
+                                lj_spica_long.h
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Class for acceleration of the lj/sdk/coul/long pair style
+  Class for acceleration of the lj/spica/coul/long pair style
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)

lib/gpu/lal_lj_spica_long_ext.cpp

@@ -1,9 +1,9 @@
 /***************************************************************************
-                                lj_sdk_long.h
+                                lj_spica_long.h
                              -------------------
                             W. Michael Brown (ORNL)
 
-  Functions for LAMMPS access to lj/sdk/coul/long acceleration functions
+  Functions for LAMMPS access to lj/spica/coul/long acceleration functions
 
  __________________________________________________________________________
     This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@@ -17,7 +17,7 @@
 #include <cassert>
 #include <cmath>
 
-#include "lal_lj_sdk_long.h"
+#include "lal_lj_spica_long.h"
 
 using namespace std;
 using namespace LAMMPS_AL;
@@ -27,7 +27,7 @@ static CGCMMLong<PRECISION,ACC_PRECISION> CMMLMF;
 // ---------------------------------------------------------------------------
 // Allocate memory on host and device and copy constants to device
 // ---------------------------------------------------------------------------
-int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
+int spical_gpu_init(const int ntypes, double **cutsq, int **cg_type,
                   double **host_lj1, double **host_lj2, double **host_lj3,
                   double **host_lj4, double **offset, double *special_lj,
                   const int inum, const int nall, const int max_nbors,
@@ -44,7 +44,7 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
   int gpu_rank=CMMLMF.device->gpu_rank();
   int procs_per_gpu=CMMLMF.device->procs_per_gpu();
 
-  CMMLMF.device->init_message(screen,"lj/sdk/coul/long",first_gpu,last_gpu);
+  CMMLMF.device->init_message(screen,"lj/spica/coul/long",first_gpu,last_gpu);
 
   bool message=false;
   if (CMMLMF.device->replica_me()==0 && screen)
@@ -93,11 +93,11 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
   return init_ok;
 }
 
-void sdkl_gpu_clear() {
+void spical_gpu_clear() {
   CMMLMF.clear();
 }
 
-int** sdkl_gpu_compute_n(const int ago, const int inum_full,
+int** spical_gpu_compute_n(const int ago, const int inum_full,
                          const int nall, double **host_x, int *host_type,
                          double *sublo, double *subhi, tagint *tag, int **nspecial,
                          tagint **special, const bool eflag, const bool vflag,
@@ -111,7 +111,7 @@ int** sdkl_gpu_compute_n(const int ago, const int inum_full,
                         host_q,boxlo,prd);
 }
 
-void sdkl_gpu_compute(const int ago, const int inum_full, const int nall,
+void spical_gpu_compute(const int ago, const int inum_full, const int nall,
                       double **host_x, int *host_type, int *ilist, int *numj,
                       int **firstneigh, const bool eflag, const bool vflag,
                       const bool eatom, const bool vatom, int &host_start,
@@ -122,7 +122,7 @@ void sdkl_gpu_compute(const int ago, const int inum_full, const int nall,
                 host_q,nlocal,boxlo,prd);
 }
 
-double sdkl_gpu_bytes() {
+double spical_gpu_bytes() {
   return CMMLMF.host_memory_usage();
 }
 

lib/gpu/lal_pre_cuda_hip.h

@@ -30,7 +30,7 @@
 // -------------------------------------------------------------------------
 
 
-#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
 #define CONFIG_ID 303
 #define SIMD_SIZE 64
 #else
@@ -112,7 +112,7 @@
 //                         KERNEL MACROS - TEXTURES
 // -------------------------------------------------------------------------
 
-#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
 #define _texture(name, type)  __device__ type* name
 #define _texture_2d(name, type)  __device__ type* name
 #else
@@ -134,6 +134,9 @@
     int2 qt = tex1Dfetch(q_tex,i);                       \
     ans=__hiloint2double(qt.y, qt.x);                    \
   }
+  #elseif  defined(__HIP_PLATFORM_SPIRV__)
+      #define fetch4(ans,i,pos_tex) tex1Dfetch(&ans, pos_tex, i);
+      #define fetch(ans,i,q_tex) tex1Dfetch(&ans, q_tex,i);
   #else
     #define fetch4(ans,i,pos_tex) ans=tex1Dfetch(pos_tex, i);
     #define fetch(ans,i,q_tex) ans=tex1Dfetch(q_tex,i);
@@ -152,7 +155,7 @@
   #define mu_tex mu_
 #endif
 
-#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
 
 #undef fetch4
 #undef fetch
@@ -209,7 +212,7 @@
 #endif
 #endif
 
-#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
+#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
 
   #ifdef _SINGLE_SINGLE
     #define shfl_down __shfl_down

lib/kokkos/bin/nvcc_wrapper

@@ -306,13 +306,13 @@ do
   -A)
     ;;
 
-  #strip of -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98
+  #strip off -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98
   -std=c++98|--std=c++98)
     ;;
-  #strip of pedantic because it produces endless warnings about #LINE added by the preprocessor
+  #strip off pedantic because it produces endless warnings about #LINE added by the preprocessor
-  -pedantic|-Wpedantic|-ansi)
+  -pedantic|-pedantic-errors|-Wpedantic|-ansi)
     ;;
-  #strip of -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C"
+  #strip off -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C"
   -Woverloaded-virtual)
     ;;
   #strip -Xcompiler because we add it

lib/linalg/dasum.f

@@ -54,8 +54,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level1
 *
 *> \par Further Details:
@@ -71,10 +69,9 @@
 *  =====================================================================
       DOUBLE PRECISION FUNCTION DASUM(N,DX,INCX)
 *
-*  -- Reference BLAS level1 routine (version 3.7.0) --
+*  -- Reference BLAS level1 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER INCX,N
@@ -128,4 +125,7 @@
       END IF
       DASUM = DTEMP
       RETURN
+*
+*     End of DASUM
+*
       END

lib/linalg/daxpy.f

@@ -73,8 +73,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level1
 *
 *> \par Further Details:
@@ -89,10 +87,9 @@
 *  =====================================================================
       SUBROUTINE DAXPY(N,DA,DX,INCX,DY,INCY)
 *
-*  -- Reference BLAS level1 routine (version 3.7.0) --
+*  -- Reference BLAS level1 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       DOUBLE PRECISION DA
@@ -149,4 +146,7 @@
          END DO
       END IF
       RETURN
+*
+*     End of DAXPY
+*
       END

lib/linalg/dbdsqr.f

@@ -166,7 +166,7 @@
 *>
 *> \param[out] WORK
 *> \verbatim
-*>          WORK is DOUBLE PRECISION array, dimension (4*N)
+*>          WORK is DOUBLE PRECISION array, dimension (4*(N-1))
 *> \endverbatim
 *>
 *> \param[out] INFO
@@ -233,18 +233,15 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2017
-*
 *> \ingroup auxOTHERcomputational
 *
 *  =====================================================================
       SUBROUTINE DBDSQR( UPLO, N, NCVT, NRU, NCC, D, E, VT, LDVT, U,
      $                   LDU, C, LDC, WORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.1) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2017
 *
 *     .. Scalar Arguments ..
       CHARACTER          UPLO

lib/linalg/dcabs1.f

@@ -40,17 +40,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level1
 *
 *  =====================================================================
       DOUBLE PRECISION FUNCTION DCABS1(Z)
 *
-*  -- Reference BLAS level1 routine (version 3.7.0) --
+*  -- Reference BLAS level1 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       COMPLEX*16 Z
@@ -63,4 +60,7 @@
 *
       DCABS1 = ABS(DBLE(Z)) + ABS(DIMAG(Z))
       RETURN
+*
+*     End of DCABS1
+*
       END

lib/linalg/dcopy.f

@@ -66,8 +66,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level1
 *
 *> \par Further Details:
@@ -82,10 +80,9 @@
 *  =====================================================================
       SUBROUTINE DCOPY(N,DX,INCX,DY,INCY)
 *
-*  -- Reference BLAS level1 routine (version 3.7.0) --
+*  -- Reference BLAS level1 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER INCX,INCY,N
@@ -143,4 +140,7 @@
          END DO
       END IF
       RETURN
+*
+*     End of DCOPY
+*
       END

lib/linalg/ddot.f

@@ -66,8 +66,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level1
 *
 *> \par Further Details:
@@ -82,10 +80,9 @@
 *  =====================================================================
       DOUBLE PRECISION FUNCTION DDOT(N,DX,INCX,DY,INCY)
 *
-*  -- Reference BLAS level1 routine (version 3.7.0) --
+*  -- Reference BLAS level1 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER INCX,INCY,N
@@ -145,4 +142,7 @@
       END IF
       DDOT = DTEMP
       RETURN
+*
+*     End of DDOT
+*
       END

lib/linalg/dgebd2.f

@@ -132,8 +132,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2017
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -189,10 +187,9 @@
 *  =====================================================================
       SUBROUTINE DGEBD2( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.1) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2017
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgebrd.f

@@ -147,8 +147,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2017
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -205,10 +203,9 @@
       SUBROUTINE DGEBRD( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, LWORK,
      $                   INFO )
 *
-*  -- LAPACK computational routine (version 3.7.1) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2017
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LWORK, M, N
@@ -227,8 +224,7 @@
 *     .. Local Scalars ..
       LOGICAL            LQUERY
       INTEGER            I, IINFO, J, LDWRKX, LDWRKY, LWKOPT, MINMN, NB,
-     $                   NBMIN, NX
+     $                   NBMIN, NX, WS
-      DOUBLE PRECISION   WS
 *     ..
 *     .. External Subroutines ..
       EXTERNAL           DGEBD2, DGEMM, DLABRD, XERBLA

lib/linalg/dgecon.f

@@ -116,18 +116,15 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK,
      $                   INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       CHARACTER          NORM

lib/linalg/dgelq2.f

@@ -33,8 +33,16 @@
 *>
 *> \verbatim
 *>
-*> DGELQ2 computes an LQ factorization of a real m by n matrix A:
+*> DGELQ2 computes an LQ factorization of a real m-by-n matrix A:
-*> A = L * Q.
+*>
+*>    A = ( L 0 ) *  Q
+*>
+*> where:
+*>
+*>    Q is a n-by-n orthogonal matrix;
+*>    L is a lower-triangular m-by-m matrix;
+*>    0 is a m-by-(n-m) zero matrix, if m < n.
+*>
 *> \endverbatim
 *
 *  Arguments:
@@ -96,8 +104,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -121,10 +127,9 @@
 *  =====================================================================
       SUBROUTINE DGELQ2( M, N, A, LDA, TAU, WORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgelqf.f

@@ -34,7 +34,15 @@
 *> \verbatim
 *>
 *> DGELQF computes an LQ factorization of a real M-by-N matrix A:
-*> A = L * Q.
+*>
+*>    A = ( L 0 ) *  Q
+*>
+*> where:
+*>
+*>    Q is a N-by-N orthogonal matrix;
+*>    L is a lower-triangular M-by-M matrix;
+*>    0 is a M-by-(N-M) zero matrix, if M < N.
+*>
 *> \endverbatim
 *
 *  Arguments:
@@ -110,8 +118,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -135,10 +141,9 @@
 *  =====================================================================
       SUBROUTINE DGELQF( M, N, A, LDA, TAU, WORK, LWORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LWORK, M, N

lib/linalg/dgelsd.f

@@ -194,8 +194,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2017
-*
 *> \ingroup doubleGEsolve
 *
 *> \par Contributors:
@@ -209,10 +207,9 @@
       SUBROUTINE DGELSD( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK,
      $                   WORK, LWORK, IWORK, INFO )
 *
-*  -- LAPACK driver routine (version 3.7.1) --
+*  -- LAPACK driver routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2017
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LDB, LWORK, M, N, NRHS, RANK

lib/linalg/dgelss.f

@@ -164,18 +164,15 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEsolve
 *
 *  =====================================================================
       SUBROUTINE DGELSS( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK,
      $                   WORK, LWORK, INFO )
 *
-*  -- LAPACK driver routine (version 3.7.0) --
+*  -- LAPACK driver routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LDB, LWORK, M, N, NRHS, RANK

lib/linalg/dgemm.f

@@ -166,8 +166,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level3
 *
 *> \par Further Details:
@@ -187,10 +185,9 @@
 *  =====================================================================
       SUBROUTINE DGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC)
 *
-*  -- Reference BLAS level3 routine (version 3.7.0) --
+*  -- Reference BLAS level3 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       DOUBLE PRECISION ALPHA,BETA
@@ -215,7 +212,7 @@
 *     ..
 *     .. Local Scalars ..
       DOUBLE PRECISION TEMP
-      INTEGER I,INFO,J,L,NCOLA,NROWA,NROWB
+      INTEGER I,INFO,J,L,NROWA,NROWB
       LOGICAL NOTA,NOTB
 *     ..
 *     .. Parameters ..
@@ -224,17 +221,15 @@
 *     ..
 *
 *     Set  NOTA  and  NOTB  as  true if  A  and  B  respectively are not
-*     transposed and set  NROWA, NCOLA and  NROWB  as the number of rows
+*     transposed and set  NROWA and NROWB  as the number of rows of  A
-*     and  columns of  A  and the  number of  rows  of  B  respectively.
+*     and  B  respectively.
 *
       NOTA = LSAME(TRANSA,'N')
       NOTB = LSAME(TRANSB,'N')
       IF (NOTA) THEN
           NROWA = M
-          NCOLA = K
       ELSE
           NROWA = K
-          NCOLA = M
       END IF
       IF (NOTB) THEN
           NROWB = K
@@ -379,6 +374,6 @@
 *
       RETURN
 *
-*     End of DGEMM .
+*     End of DGEMM
 *
       END

lib/linalg/dgemv.f

@@ -134,8 +134,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level2
 *
 *> \par Further Details:
@@ -156,10 +154,9 @@
 *  =====================================================================
       SUBROUTINE DGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY)
 *
-*  -- Reference BLAS level2 routine (version 3.7.0) --
+*  -- Reference BLAS level2 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       DOUBLE PRECISION ALPHA,BETA
@@ -325,6 +322,6 @@
 *
       RETURN
 *
-*     End of DGEMV .
+*     End of DGEMV
 *
       END

lib/linalg/dgeqr2.f

@@ -33,8 +33,17 @@
 *>
 *> \verbatim
 *>
-*> DGEQR2 computes a QR factorization of a real m by n matrix A:
+*> DGEQR2 computes a QR factorization of a real m-by-n matrix A:
-*> A = Q * R.
+*>
+*>    A = Q * ( R ),
+*>            ( 0 )
+*>
+*> where:
+*>
+*>    Q is a m-by-m orthogonal matrix;
+*>    R is an upper-triangular n-by-n matrix;
+*>    0 is a (m-n)-by-n zero matrix, if m > n.
+*>
 *> \endverbatim
 *
 *  Arguments:
@@ -96,8 +105,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -121,10 +128,9 @@
 *  =====================================================================
       SUBROUTINE DGEQR2( M, N, A, LDA, TAU, WORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgeqrf.f

@@ -34,7 +34,16 @@
 *> \verbatim
 *>
 *> DGEQRF computes a QR factorization of a real M-by-N matrix A:
-*> A = Q * R.
+*>
+*>    A = Q * ( R ),
+*>            ( 0 )
+*>
+*> where:
+*>
+*>    Q is a M-by-M orthogonal matrix;
+*>    R is an upper-triangular N-by-N matrix;
+*>    0 is a (M-N)-by-N zero matrix, if M > N.
+*>
 *> \endverbatim
 *
 *  Arguments:
@@ -86,7 +95,8 @@
 *> \param[in] LWORK
 *> \verbatim
 *>          LWORK is INTEGER
-*>          The dimension of the array WORK.  LWORK >= max(1,N).
+*>          The dimension of the array WORK.
+*>          LWORK >= 1, if MIN(M,N) = 0, and LWORK >= N, otherwise.
 *>          For optimum performance LWORK >= N*NB, where NB is
 *>          the optimal blocksize.
 *>
@@ -111,8 +121,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *> \par Further Details:
@@ -136,10 +144,9 @@
 *  =====================================================================
       SUBROUTINE DGEQRF( M, N, A, LDA, TAU, WORK, LWORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LWORK, M, N
@@ -169,10 +176,9 @@
 *
 *     Test the input arguments
 *
+      K = MIN( M, N )
       INFO = 0
       NB = ILAENV( 1, 'DGEQRF', ' ', M, N, -1, -1 )
-      LWKOPT = N*NB
-      WORK( 1 ) = LWKOPT
       LQUERY = ( LWORK.EQ.-1 )
       IF( M.LT.0 ) THEN
          INFO = -1
@@ -180,19 +186,25 @@
          INFO = -2
       ELSE IF( LDA.LT.MAX( 1, M ) ) THEN
          INFO = -4
-      ELSE IF( LWORK.LT.MAX( 1, N ) .AND. .NOT.LQUERY ) THEN
+      ELSE IF( .NOT.LQUERY ) THEN
-         INFO = -7
+         IF( LWORK.LE.0 .OR. ( M.GT.0 .AND. LWORK.LT.MAX( 1, N ) ) )
+     $      INFO = -7
       END IF
       IF( INFO.NE.0 ) THEN
          CALL XERBLA( 'DGEQRF', -INFO )
          RETURN
       ELSE IF( LQUERY ) THEN
+         IF( K.EQ.0 ) THEN
+            LWKOPT = 1
+         ELSE
+            LWKOPT = N*NB
+         END IF
+         WORK( 1 ) = LWKOPT
          RETURN
       END IF
 *
 *     Quick return if possible
 *
-      K = MIN( M, N )
       IF( K.EQ.0 ) THEN
          WORK( 1 ) = 1
          RETURN

lib/linalg/dger.f

@@ -109,8 +109,6 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup double_blas_level2
 *
 *> \par Further Details:
@@ -130,10 +128,9 @@
 *  =====================================================================
       SUBROUTINE DGER(M,N,ALPHA,X,INCX,Y,INCY,A,LDA)
 *
-*  -- Reference BLAS level2 routine (version 3.7.0) --
+*  -- Reference BLAS level2 routine --
 *  -- Reference BLAS is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       DOUBLE PRECISION ALPHA
@@ -222,6 +219,6 @@
 *
       RETURN
 *
-*     End of DGER  .
+*     End of DGER
 *
       END

lib/linalg/dgesv.f

@@ -115,17 +115,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEsolve
 *
 *  =====================================================================
       SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO )
 *
-*  -- LAPACK driver routine (version 3.7.0) --
+*  -- LAPACK driver routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LDB, N, NRHS

lib/linalg/dgesvd.f

@@ -203,18 +203,15 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date April 2012
-*
 *> \ingroup doubleGEsing
 *
 *  =====================================================================
       SUBROUTINE DGESVD( JOBU, JOBVT, M, N, A, LDA, S, U, LDU,
      $                   VT, LDVT, WORK, LWORK, INFO )
 *
-*  -- LAPACK driver routine (version 3.7.0) --
+*  -- LAPACK driver routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     April 2012
 *
 *     .. Scalar Arguments ..
       CHARACTER          JOBU, JOBVT

lib/linalg/dgetf2.f

@@ -101,17 +101,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       SUBROUTINE DGETF2( M, N, A, LDA, IPIV, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgetrf.f

@@ -101,17 +101,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgetrf2.f

@@ -106,17 +106,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       RECURSIVE SUBROUTINE DGETRF2( M, N, A, LDA, IPIV, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, M, N

lib/linalg/dgetri.f

@@ -107,17 +107,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       SUBROUTINE DGETRI( N, A, LDA, IPIV, WORK, LWORK, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       INTEGER            INFO, LDA, LWORK, N

lib/linalg/dgetrs.f

@@ -114,17 +114,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date December 2016
-*
 *> \ingroup doubleGEcomputational
 *
 *  =====================================================================
       SUBROUTINE DGETRS( TRANS, N, NRHS, A, LDA, IPIV, B, LDB, INFO )
 *
-*  -- LAPACK computational routine (version 3.7.0) --
+*  -- LAPACK computational routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     December 2016
 *
 *     .. Scalar Arguments ..
       CHARACTER          TRANS

lib/linalg/disnan.f

@@ -52,17 +52,14 @@
 *> \author Univ. of Colorado Denver
 *> \author NAG Ltd.
 *
-*> \date June 2017
-*
 *> \ingroup OTHERauxiliary
 *
 *  =====================================================================
       LOGICAL FUNCTION DISNAN( DIN )
 *
-*  -- LAPACK auxiliary routine (version 3.7.1) --
+*  -- LAPACK auxiliary routine --
 *  -- LAPACK is a software package provided by Univ. of Tennessee,    --
 *  -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
-*     June 2017
 *
 *     .. Scalar Arguments ..
       DOUBLE PRECISION, INTENT(IN) :: DIN