Merge branch 'master' into user-intel-update (05847a0e) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+8 −2

Original line number	Diff line number	Diff line
		@@ -37,6 +37,10 @@ enable_language(CXX)
		#####################################################################
		include(CheckCCompilerFlag)

		if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
		endif()

		########################################################################
		# User input options #
		########################################################################
		@@ -76,7 +80,7 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
		option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
		if(LAMMPS_EXCEPTIONS)
		add_definitions(-DLAMMPS_EXCEPTIONS)
		set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
		set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
		endif()

		set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
		@@ -665,7 +669,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
		############################################
		add_library(lammps ${LIB_SOURCES})
		target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
		if(LAMMPS_DEPS)
		add_dependencies(lammps ${LAMMPS_DEPS})
		endif()
		set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
		if(BUILD_SHARED_LIBS)
		set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})

+2 −1

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		@@ -705,7 +705,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
		quantum forces calculated by LATTE.

		More information on LATTE can be found at this web site:
		"https://github.com/lanl/LATTE"_#latte_home. A brief technical
		"https://github.com/lanl/LATTE"_latte_home. A brief technical
		description is given with the "fix latte"_fix_latte.html command.

		:link(latte_home,https://github.com/lanl/LATTE)
		@@ -728,6 +728,7 @@ make lib-latte args="-b" # download and build in lib/latte/LATTE-
		make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
		make lib-latte args="-b -m gfortran" # download and build in lib/latte and
		# copy Makefile.lammps.gfortran to Makefile.lammps
		:pre

		Note that 3 symbolic (soft) links, "includelink" and "liblink" and
		"filelink", are created in lib/latte to point into the LATTE home dir.

+5 −5

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		@@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
		integrals are parameterized using a Slater-Koster tight-binding
		approach. This procedure, which usually is referred to as the DFTB
		method has been described in detail by ("Elstner"_#Elstner) and
		("Finnis"_#Finnis) and coworkers.
		("Finnis"_#Finnis2) and coworkers.

		The work of the LATTE developers follows that of Elstner closely with
		respect to the physical model. However, the development of LATTE is
		@@ -173,7 +173,7 @@ M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
		M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
		7260 (1998).

		:link(Finnis)
		:link(Finnis2)
		[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
		Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).

		@@ -197,11 +197,11 @@ J. Sci. Comput. 36 (2), 147-170, (2014).
		[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
		141, 164123, (2014).

		:link(Niklasson2014)
		:link(Niklasson2017)
		[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).

		:link(Niklasson2012)
		[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
		:link(Cawkwell2012)
		[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
		(17), 174308 (2012).

		:link(Negre2016)

+2 −2

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		@@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:

		Fnudge_parallel = {Kspring} * (\|Ri+1 - Ri\| - \|Ri - Ri-1\|) :pre

		Note that in this case the specified {Kspring) is in force/distance
		Note that in this case the specified {Kspring} is in force/distance
		units.

		With a value of {ideal}, the spring force is computed as suggested in
		@@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
		RDideal is the ideal RD for which all the images are equally spaced.
		I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
		I is the replica number). The meanDist is the average distance
		between replicas. Note that in this case the specified {Kspring) is
		between replicas. Note that in this case the specified {Kspring} is
		in force units.

		Note that the {ideal} form of nudging can often be more effective at

+1 −0