Merge branch 'team' into comm_squash

endif()

if(PKG_KIM)

  option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)

  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)

  if(DOWNLOAD_KIM)

    message(STATUS "KIM-API v1 download requested - we will build our own")

    message(STATUS "KIM-API v2 download requested - we will build our own")

    enable_language(C)

    enable_language(Fortran)

    include(ExternalProject)

    ExternalProject_Add(kim_build

      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz

      URL_MD5 9f66efc128da33039e30659f36fc6d00

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.0.txz

      URL_MD5 1ff8f563ad5991f7a2a25b35a13d7308

      BINARY_DIR build

      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}

                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>

                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}

      )

    ExternalProject_get_property(kim_build INSTALL_DIR)

    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)

    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)

    set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)

    set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})

    list(APPEND LAMMPS_DEPS kim_build)

  else()

    find_package(KIM)

    if(NOT KIM_FOUND)

      message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")

    find_package(KIM-API-V2)

    if(NOT KIM-API-V2_FOUND)

      message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")

    endif()

  endif()

  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})

  include_directories(${KIM_INCLUDE_DIRS})

  list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")

  include_directories(${KIM-API-V2_INCLUDE_DIRS})

endif()

if(PKG_MESSAGE)

#

# CDDL HEADER START

#

# The contents of this file are subject to the terms of the Common Development

# and Distribution License Version 1.0 (the "License").

#

# You can obtain a copy of the license at

# http://www.opensource.org/licenses/CDDL-1.0.  See the License for the

# specific language governing permissions and limitations under the License.

#

# When distributing Covered Code, include this CDDL HEADER in each file and

# include the License file in a prominent location with the name LICENSE.CDDL.

# If applicable, add the following below this CDDL HEADER, with the fields

# enclosed by brackets "[]" replaced with your own identifying information:

#

# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.

#

# CDDL HEADER END

#

#

# Copyright (c) 2013--2018, Regents of the University of Minnesota.

# All rights reserved.

#

# Contributors:

#    Richard Berger

#    Christoph Junghans

#    Ryan S. Elliott

#

# - Find KIM-API-V2

#

# sets standard pkg_check_modules variables plus:

#

# KIM-API-V2-CMAKE_C_COMPILER

# KIM-API-V2-CMAKE_CXX_COMPILER

# KIM-API-V2-CMAKE_Fortran_COMPILER

#

find_package(PkgConfig REQUIRED)

include(FindPackageHandleStandardArgs)

pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)

pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)

pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)

pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)

# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE

# if all listed variables are TRUE

find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)

# - Find kim

# Find the native KIM headers and libraries.

#

#  KIM_INCLUDE_DIRS - where to find kim.h, etc.

#  KIM_LIBRARIES    - List of libraries when using kim.

#  KIM_FOUND        - True if kim found.

#

find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)

find_library(KIM_LIBRARY NAMES kim-api-v1)

set(KIM_LIBRARIES ${KIM_LIBRARY})

set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})

include(FindPackageHandleStandardArgs)

# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE

# if all listed variables are TRUE

find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)

mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

/old

/html

/latex

/spelling

	@echo "Please use \`make <target>' where <target> is one of"

	@echo "  html       create HTML doc pages in html dir"

	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"

	@echo "  old        create old-style HTML doc pages in old dir"

	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"

	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"

	@echo "  epub       create ePUB format manual for e-book readers"

	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"

	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe

clean:

	rm -rf $(RSTDIR) html old epub

	rm -rf $(RSTDIR) html old epub latex

	rm -rf spelling

clean-spelling:

	@ebook-convert LAMMPS.epub LAMMPS.mobi

	@echo "Conversion finished. The MOBI manual file is created."

pdf: utils/txt2html/txt2html.exe

pdf: $(OBJECTS) $(ANCHORCHECK)

	@(\

                . $(VENV)/bin/activate ;\

                cp -r src/* $(RSTDIR)/ ;\

                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\

                echo "############################################" ;\

                doc_anchor_check src/*.txt ;\

                echo "############################################" ;\

                deactivate ;\

	)

	@cd latex && \

          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \

	  mv temp Makefile && \

	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \

	  mv tmp.tex LAMMPS.tex && \

	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \

	  mv tmp.tex LAMMPS.tex && \

	  make && \

	  make && \

	  mv LAMMPS.pdf ../Manual.pdf && \

	  cd ../; 

	@(\

		set -e; \

		cd src/Developer; \

		pdflatex developer; \

		pdflatex developer; \

		mv developer.pdf ../../Developer.pdf; \

		cd ..; \

		../utils/txt2html/txt2html.exe -b *.txt; \

		htmldoc --batch lammps.book;          \

		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \

			do grep -q ^$$s lammps.book || \

			echo WARNING: doc file $$s missing in src/lammps.book; done; \

		rm *.html; \

		cd ../../; \

	)

	@rm -rf latex/_sources

	@rm -rf latex/PDF

	@rm -rf latex/USER

	@cp -r src/PDF latex/PDF

	@cp -r src/USER latex/USER

	@rm -rf latex/PDF/.[sg]*

	@rm -rf latex/USER/.[sg]*

	@rm -rf latex/USER/*/.[sg]*

	@rm -rf latex/USER/*/*.[sg]*

	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."

old: utils/txt2html/txt2html.exe

	@rm -rf old

	  cp Eqs/*.jpg ../old/Eqs; \

	  cp JPG/* ../old/JPG; \

	  cp PDF/* ../old/PDF;

	@(      set -e;\

		cd src/Developer; \

		pdflatex developer; \

		pdflatex developer; \

		mv developer.pdf ../../old/Developer.pdf; \

		cd ../../old; \

	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \

			do grep -q ^$$s ../src/lammps.book || \

			echo WARNING: doc file $$s missing in src/lammps.book; done; \

		htmldoc --batch ../src/lammps.book;          \

	)

fetch:

	@rm -rf html_www Manual_www.pdf Developer_www.pdf