Merge branch 'master' into fix-compiler-warnings (68adc56e) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+6 −10

Changes for cmake/CMakeLists.txt: 6 added lines, 10 removed lines.
Original line number	Diff line number	Diff line
		@@ -322,13 +322,14 @@ endif()
		include(Packages/KSPACE)
		include(Packages/PYTHON)
		include(Packages/VORONOI)
		include(Packages/USER-SCAFACOS)
		include(Packages/USER-PLUMED)
		include(Packages/USER-COLVARS)
		include(Packages/USER-MOLFILE)
		include(Packages/USER-NETCDF)
		include(Packages/USER-SMD)
		include(Packages/USER-QUIP)
		include(Packages/USER-PLUMED)
		include(Packages/USER-QMMM)
		include(Packages/USER-QUIP)
		include(Packages/USER-SCAFACOS)
		include(Packages/USER-SMD)
		include(Packages/USER-VTK)
		include(Packages/KIM)
		include(Packages/LATTE)
		@@ -418,8 +419,7 @@ endforeach()
		##############################################
		# add lib sources of (simple) enabled packages
		############################################
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		USER-QMMM)
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
		if(PKG_${SIMPLE_LIB})
		string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
		string(TOLOWER "${PKG_LIB}" PKG_LIB)
		@@ -433,10 +433,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
		elseif(PKG_LIB STREQUAL h5md)
		target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
		elseif(PKG_LIB STREQUAL colvars)
		target_compile_options(colvars PRIVATE -DLEPTON)
		target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
		target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
		else()
		target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
		endif()

cmake/Modules/Packages/USER-COLVARS.cmake

0 → 100644

+42 −0

Changes for cmake/Modules/Packages/USER-COLVARS.cmake: 42 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		if(PKG_USER-COLVARS)

		set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)

		file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)

		# Build Lepton by default
		set(COLVARS_LEPTON_DEFAULT ON)
		# but not if C++11 is disabled per user request
		if(DEFINED DISABLE_CXX11_REQUIREMENT)
		if(DISABLE_CXX11_REQUIREMENT)
		set(COLVARS_LEPTON_DEFAULT OFF)
		endif()
		endif()

		option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})

		# Verify that the user's choice is consistent
		if(DEFINED DISABLE_CXX11_REQUIREMENT)
		if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
		message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
		endif()
		endif()

		if(COLVARS_LEPTON)
		set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
		file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
		add_library(lepton STATIC ${LEPTON_SOURCES})
		target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
		endif()

		add_library(colvars STATIC ${COLVARS_SOURCES})
		target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
		list(APPEND LAMMPS_LINK_LIBS colvars)

		if(COLVARS_LEPTON)
		list(APPEND LAMMPS_LINK_LIBS lepton)
		target_compile_options(colvars PRIVATE -DLEPTON)
		target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
		endif()

		endif()

cmake/presets/most.cmake

+1 −1

Changes for cmake/presets/most.cmake: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@ set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
		PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
		USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
		USER-DRUDE USER-FEP USER-MEAMC USER-MESO
		USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
		USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
		USER-SPH USER-SMD USER-UEF USER-YAFF)

		foreach(PKG ${ALL_PACKAGES})

doc/src/Errors_warnings.txt

+44 −0

Changes for doc/src/Errors_warnings.txt: 44 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -47,6 +47,11 @@ too far away. :dd

		Self-explanatory. :dd

		{Angles are defined but no angle style is set} :dt

		The topology contains angles, but there are no angle forces computed
		since there was no angle_style command. :dd

		{Atom style in data file differs from currently defined atom style} :dt

		Self-explanatory. :dd
		@@ -73,6 +78,11 @@ short or the bond has blown apart and an atom is too far away. :dd

		Self-explanatory. :dd

		{Bonds are defined but no bond style is set} :dt

		The topology contains bonds, but there are no bond forces computed
		since there was no bond_style command. :dd

		{Bond/angle/dihedral extent > half of periodic box length} :dt

		This is a restriction because LAMMPS can be confused about which image
		@@ -186,6 +196,11 @@ to check your simulation geometry. :dd

		Self-explanatory. :dd

		{Dihedrals are defined but no dihedral style is set} :dt

		The topology contains dihedrals, but there are no dihedral forces computed
		since there was no dihedral_style command. :dd

		{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt

		If the fix changes the timestep, the dump dcd file will not
		@@ -352,6 +367,11 @@ to check your simulation geometry. :dd

		Self-explanatory. :dd

		{Impropers are defined but no improper style is set} :dt

		The topology contains impropers, but there are no improper forces computed
		since there was no improper_style command. :dd

		{Inconsistent image flags} :dt

		The image flags for a pair on bonded atoms appear to be inconsistent.
		@@ -407,6 +427,30 @@ This library function cannot be used if atom IDs are not defined or
		are not consecutively numbered, or if no atom map is defined. See the
		atom_modify command for details about atom maps. :dd

		{Likewise 1-2 special neighbor interactions != 1.0} :dt

		The topology contains bonds, but there is no bond style defined
		and a 1-2 special neighbor scaling factor was not 1.0. This
		means that pair style interactions may have scaled or missing
		pairs in the neighbor list in expectation of interactions for
		those pairs being computed from the bond style. :dd

		{Likewise 1-3 special neighbor interactions != 1.0} :dt

		The topology contains angles, but there is no angle style defined
		and a 1-3 special neighbor scaling factor was not 1.0. This
		means that pair style interactions may have scaled or missing
		pairs in the neighbor list in expectation of interactions for
		those pairs being computed from the angle style. :dd

		{Likewise 1-4 special neighbor interactions != 1.0} :dt

		The topology contains dihedrals, but there is no dihedral style defined
		and a 1-4 special neighbor scaling factor was not 1.0. This
		means that pair style interactions may have scaled or missing
		pairs in the neighbor list in expectation of interactions for
		those pairs being computed from the dihedral style. :dd

		{Lost atoms via change_box: original %ld current %ld} :dt

		The command options you have used caused atoms to be lost. :dd

doc/src/Tools.txt

+10 −0

Changes for doc/src/Tools.txt: 10 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -87,6 +87,7 @@ Miscellaneous tools :h3
		"emacs"_#emacs,
		"i-pi"_#ipi,
		"kate"_#kate,
		"singularity"_#singularity_tool,
		"vim"_#vim :tb(c=5,ea=c,a=l)

		:line
		@@ -542,6 +543,15 @@ Ivanov, at University of Iceland (ali5 at hi.is).

		:line

		singularity tool :h4,link(singularity_tool)

		The singularity sub-directory contains container definitions files
		that can be used to build container images for building and testing
		LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
		container software. Contributions for additional variants are welcome.

		:line

		vim tool :h4,link(vim)

		The files in the tools/vim directory are add-ons to the VIM editor

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