[pull] develop from lammps:develop

.github/release_steps.md

@@ -187,23 +187,8 @@ attached to the GitHub release page.
 
 #### LAMMPS Online Manual
 
-Creating the online docs requires setting some environment variables to have
-the extra box at the bottom of the navigation bar included that allows to
-switch between release, stable, and develop branch versions of the manual.
-Also the search box should use Google search instead of the javascript search.
-
-``` sh
-cd lammps-release
-make -C doc clean
-make -C doc upgrade
-env LAMMPS_WEBSITE_BUILD=1 LAMMPS_WEBSITE_BUILD_VERSION=release LAMMPS_WEBSITE_BASEURL="https://docs.lammps.org/" \
-    make -C doc html WEB_SEARCH=YES
-make -C doc pdf
-mv doc/Manual.pdf doc/html
-rsync -arpv doc/html/ www.lammps.org:/var/www/lammps/docs/release-new
-
-Then log into www.lammps.org and move the current folder away and
-the new folder in its place and update permissions.
+The online manual pages are now automatically updated by the scripts in
+the [lammps-docs](https://github.com/lammps/lammps-docs/) repository.
 
 #### Clean up:
 

cmake/CMakeLists.txt

@@ -320,7 +320,6 @@ set(STANDARD_PACKAGES
   ML-POD
   ML-QUIP
   ML-RUNNER
-  ML-RANN
   ML-SNAP
   ML-UF3
   MOFFF

cmake/Modules/Packages/ML-QUIP.cmake

@@ -20,16 +20,16 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
     # quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
-    string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
+    string(REGEX REPLACE -std=f[0-9]+ "" _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt}\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
-    set(temp "${temp}F90FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
-    set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
-    set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
+    set(temp "${temp}F90FLAGS += -std=gnu -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fmax-stack-var-size=6553600 -fPIC\n")
+    set(temp "${temp}F95FLAGS += -std=gnu -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fmax-stack-var-size=6553600 -fPIC\n")
+    set(temp "${temp}F77FLAGS += -std=gnu -x f77-cpp-input -fno-second-underscore -fmax-stack-var-size=6553600 -fPIC\n")
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch -DPROTOTYPES=1\nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -std=gnu89 -fPIC -Wno-return-mismatch -DPROTOTYPES=1\nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")

cmake/Modules/StyleHeaderUtils.cmake

@@ -45,7 +45,7 @@ function(FindStyleHeadersExt path style_class extension headers sources)
 endfunction(FindStyleHeadersExt)
 
 function(CreateStyleHeader path filename)
-    set(temp "")
+    set(temp "// File autogenerated by CMake\n")
     if(ARGC GREATER 2)
         list(REMOVE_AT ARGV 0 1)
         set(header_list)
@@ -223,7 +223,7 @@ function(RegisterPackages search_path)
 endfunction(RegisterPackages)
 
 function(CreatePackagesHeader path filename)
-  set(temp "")
+  set(temp "// File autogenerated by CMake\n")
   if(ARGC GREATER 2)
     list(REMOVE_AT ARGV 0 1)
     foreach(FNAME ${ARGV})

doc/Makefile

@@ -76,6 +76,7 @@ help:
 	@echo "  char_check    check for non-ASCII characters"
 	@echo "  role_check    check for misformatted role keywords"
 	@echo "  link_check    check external links in the manual"
+	@echo "  extract_check check extract() function consistency with tables in the manual"
 	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
@@ -276,6 +277,13 @@ role_check :
 	@( env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} && exit 1 || : )
 
+extract_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		$(PYTHON) utils/check-fix-adapt-tables.py --root .. ;\
+		deactivate ;\
+	)
+
 upgrade: $(VENV)
 	@(\
 		. $(VENV)/bin/activate; \

doc/doxygen/Doxyfile.in

@@ -431,6 +431,8 @@ INPUT                  = @LAMMPS_SOURCE_DIR@/utils.cpp                 \
                          @LAMMPS_SOURCE_DIR@/text_file_reader.h        \
                          @LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \
                          @LAMMPS_SOURCE_DIR@/potential_file_reader.h   \
+                         @LAMMPS_SOURCE_DIR@/stl_reader.cpp            \
+                         @LAMMPS_SOURCE_DIR@/stl_reader.h              \
                          @LAMMPS_SOURCE_DIR@/label_map.cpp             \
                          @LAMMPS_SOURCE_DIR@/label_map.h               \
                          @LAMMPS_SOURCE_DIR@/my_page.cpp               \