Merge pull request #68 from lammps/master (4b11e436) · Commits · 郑智淋 / lammps

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -26,6 +26,7 @@ vgcore.*
		.vagrant
		\#*#
		.#*
		.vscode

		.DS_Store
		.DS_Store?

cmake/CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -739,7 +739,7 @@ if(PKG_KSPACE)
		else()
		message(STATUS "Using double precision FFTs")
		endif()
		if(FFT_FFTW_THREADS)
		if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
		message(STATUS "Using threaded FFTs")
		else()
		message(STATUS "Using non-threaded FFTs")

cmake/Modules/Packages/KSPACE.cmake

+5 −1

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ if(PKG_KSPACE)
		include_directories(${${FFTW}_INCLUDE_DIRS})
		list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
		if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
		option(FFT_FFTW_THREADS "Use threaded FFT library" ON)
		option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
		else()
		option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
		endif()
		@@ -38,6 +38,10 @@ if(PKG_KSPACE)
		elseif(FFT STREQUAL "MKL")
		find_package(MKL REQUIRED)
		add_definitions(-DFFT_MKL)
		option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
		if(FFT_MKL_THREADS)
		add_definitions(-DFFT_MKL_THREADS)
		endif()
		include_directories(${MKL_INCLUDE_DIRS})
		list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
		else()

cmake/Modules/Packages/USER-PLUMED.cmake

+2 −2

Original line number	Diff line number	Diff line
		@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
		message(STATUS "PLUMED download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(plumed_build
		URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
		URL_MD5 de30d6e7c2dcc0973298e24a6da24286
		URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
		URL_MD5 204d2edae58d9b10ba3ad460cad64191
		BUILD_IN_SOURCE 1
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
		${CONFIGURE_REQUEST_PIC}

doc/Makefile

+9 −17

Original line number	Diff line number	Diff line
		@@ -3,7 +3,6 @@
		SHELL = /bin/bash
		BUILDDIR = ${CURDIR}
		RSTDIR = $(BUILDDIR)/src
		TXTDIR = $(BUILDDIR)/txt
		VENV = $(BUILDDIR)/docenv
		TXT2RST = $(VENV)/bin/txt2rst
		ANCHORCHECK = $(VENV)/bin/rst_anchor_check
		@@ -28,8 +27,6 @@ HAS_VIRTUALENV = YES
		endif

		SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
		SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/.txt))
		OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)

		.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check

		@@ -61,9 +58,9 @@ clean:
		clean-spelling:
		rm -rf spelling

		rst: clean $(OBJECTS) $(ANCHORCHECK)
		rst: clean $(ANCHORCHECK)

		html: $(OBJECTS) $(ANCHORCHECK)
		html: $(ANCHORCHECK)
		@(\
		. $(VENV)/bin/activate ;\
		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
		@@ -78,15 +75,18 @@ html: $(OBJECTS) $(ANCHORCHECK)
		@rm -rf html/_sources
		@rm -rf html/PDF
		@rm -rf html/USER
		@rm -rf html/JPG
		@cp -r src/PDF html/PDF
		@cp -r src/USER html/USER
		@mkdir -p html/JPG
		@cp `grep -A2 '\.\. image::' src/.rst \| grep ':target:' \| sed -e 's,.:target: JPG/,src/JPG/,' \| sort \| uniq` html/JPG/
		@rm -rf html/PDF/.[sg]*
		@rm -rf html/USER/.[sg]*
		@rm -rf html/USER//.[sg]
		@rm -rf html/USER//.[sg]*
		@echo "Build finished. The HTML pages are in doc/html."

		spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
		spelling: utils/sphinx-config/false_positives.txt
		@(\
		. $(VENV)/bin/activate ;\
		pip install sphinxcontrib-spelling ;\
		@@ -96,7 +96,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
		)
		@echo "Spell check finished."

		epub: $(OBJECTS)
		epub:
		@mkdir -p epub/JPG
		@rm -f LAMMPS.epub
		@cp src/JPG/lammps-logo.png epub/
		@@ -115,7 +115,7 @@ mobi: epub
		@ebook-convert LAMMPS.epub LAMMPS.mobi
		@echo "Conversion finished. The MOBI manual file is created."

		pdf: $(OBJECTS) $(ANCHORCHECK)
		pdf: $(ANCHORCHECK)
		@(\
		cd src/Developer; \
		pdflatex developer; \
		@@ -167,7 +167,7 @@ fetch:
		anchor_check : $(ANCHORCHECK)
		@(\
		. $(VENV)/bin/activate ;\
		rst_anchor_check src/*.txt ;\
		rst_anchor_check src/*.rst ;\
		deactivate ;\
		)

		@@ -180,14 +180,6 @@ style_check :

		# ------------------------------------------

		$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
		@(\
		mkdir -p $(RSTDIR) ; \
		. $(VENV)/bin/activate ;\
		txt2rst -v $< > $@ ;\
		deactivate ;\
		)

		$(VENV):
		@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
		@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi

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