Loading doc/src/Section_howto.txt +0 −1 Original line number Diff line number Diff line Loading @@ -2954,7 +2954,6 @@ property/atom"_compute_property_atom.html. It enables to output all the per atom magnetic quantities. Typically, the orientation of a given magnetic spin, or the magnetic force acting on this spin. :line :line Loading doc/src/atom_style.txt +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ {sphere} or {tri} or {template} or {hybrid} or {spin} :ulb,l {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles Loading doc/src/fix_rigid.txt +11 −13 Original line number Diff line number Diff line Loading @@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. Bodystyle {custom} is similar to bodystyle {molecule}, however some custom properties are used to group atoms into rigid bodies. The special case for molecule/body ID = 0 is not available. Possible custom properties are an integer property associated with atoms through "fix property/atom"_fix_property_atom.html or an atom style variable or an atomfile style variable. For the latter two, the variable value will be rounded to an integer and then rigid bodies defined from those values. For bodystyle {group}, each of the listed groups is treated as a separate rigid body. Only atoms that are also in the fix group are included in each rigid body. This option is only allowed for the {rigid} styles. Bodystyle {custom} is similar to bodystyle {molecule} except that it is more flexible in using other per-atom properties to define the sets of atoms that form rigid bodies. An integer vector defined by the "fix property/atom"_fix_property_atom.txt command can be used. Or an "atom-style or atomfile-style variable"_variable.html can be used; the floating-point value produced by the variable is rounded to an integer. As with bondstyle {molecule}, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. NOTE: To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the Loading src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl 0 → 100644 +121 −0 Original line number Diff line number Diff line # g++_openmpi = OpenMPI with compiler set to GNU g++ SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler #export OMPI_CXX = armclang++ CC = mpicxx CCFLAGS = -O3 -mcpu=native SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O LIB = SIZE = size ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings # see possible settings in Section 2.2 (step 4) of manual LMP_INC = -DLAMMPS_GZIP # MPI library # see discussion in Section 2.2 (step 5) of manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 MPI_PATH = MPI_LIB = # FFT library # see discussion in Section 2.2 (step 6) of manaul # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW FFT_PATH = -L$(ARMPL_LIBRARIES) FFT_LIB = -larmpl_lp64 # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual # only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC # INC = path(s) for jpeglib.h and/or png.h # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # do not edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) # Path to src files vpath %.cpp .. vpath %.h .. # Link target $(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library targets lib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ $(OBJ) $(EXTRA_LIB) $(LIB) # Compilation rules %.o:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ %.o:%.cu $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< # Individual dependencies depend : fastdep.exe $(SRC) @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c cc -O -o $@ $< sinclude .depend src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl 0 → 100644 +120 −0 Original line number Diff line number Diff line # arm_serial = Arm armclang compiler, no MPI SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler CC = armclang++ CCFLAGS = -O3 -mcpu=native SHFLAGS = -fPIC DEPFLAGS = -M LINK = armclang++ LINKFLAGS = -g -O LIB = SIZE = size ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings # see possible settings in Section 2.2 (step 4) of manual LMP_INC = -DLAMMPS_GZIP # MPI library # see discussion in Section 2.2 (step 5) of manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = -L../STUBS MPI_LIB = -lmpi_stubs # FFT library # see discussion in Section 2.2 (step 6) of manaul # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW FFT_PATH = -L$(ARMPL_LIBRARIES) FFT_LIB = -larmpl_lp64 # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual # only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC # INC = path(s) for jpeglib.h and/or png.h # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # do not edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) # Path to src files vpath %.cpp .. vpath %.h .. # Link target $(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library targets lib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ $(OBJ) $(EXTRA_LIB) $(LIB) # Compilation rules %.o:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ %.o:%.cu $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< # Individual dependencies depend : fastdep.exe $(SRC) @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c cc -O -o $@ $< sinclude .depend Loading
doc/src/Section_howto.txt +0 −1 Original line number Diff line number Diff line Loading @@ -2954,7 +2954,6 @@ property/atom"_compute_property_atom.html. It enables to output all the per atom magnetic quantities. Typically, the orientation of a given magnetic spin, or the magnetic force acting on this spin. :line :line Loading
doc/src/atom_style.txt +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ {sphere} or {tri} or {template} or {hybrid} or {spin} :ulb,l {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles Loading
doc/src/fix_rigid.txt +11 −13 Original line number Diff line number Diff line Loading @@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. Bodystyle {custom} is similar to bodystyle {molecule}, however some custom properties are used to group atoms into rigid bodies. The special case for molecule/body ID = 0 is not available. Possible custom properties are an integer property associated with atoms through "fix property/atom"_fix_property_atom.html or an atom style variable or an atomfile style variable. For the latter two, the variable value will be rounded to an integer and then rigid bodies defined from those values. For bodystyle {group}, each of the listed groups is treated as a separate rigid body. Only atoms that are also in the fix group are included in each rigid body. This option is only allowed for the {rigid} styles. Bodystyle {custom} is similar to bodystyle {molecule} except that it is more flexible in using other per-atom properties to define the sets of atoms that form rigid bodies. An integer vector defined by the "fix property/atom"_fix_property_atom.txt command can be used. Or an "atom-style or atomfile-style variable"_variable.html can be used; the floating-point value produced by the variable is rounded to an integer. As with bondstyle {molecule}, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. NOTE: To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the Loading
src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl 0 → 100644 +121 −0 Original line number Diff line number Diff line # g++_openmpi = OpenMPI with compiler set to GNU g++ SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler #export OMPI_CXX = armclang++ CC = mpicxx CCFLAGS = -O3 -mcpu=native SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O LIB = SIZE = size ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings # see possible settings in Section 2.2 (step 4) of manual LMP_INC = -DLAMMPS_GZIP # MPI library # see discussion in Section 2.2 (step 5) of manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 MPI_PATH = MPI_LIB = # FFT library # see discussion in Section 2.2 (step 6) of manaul # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW FFT_PATH = -L$(ARMPL_LIBRARIES) FFT_LIB = -larmpl_lp64 # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual # only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC # INC = path(s) for jpeglib.h and/or png.h # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # do not edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) # Path to src files vpath %.cpp .. vpath %.h .. # Link target $(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library targets lib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ $(OBJ) $(EXTRA_LIB) $(LIB) # Compilation rules %.o:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ %.o:%.cu $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< # Individual dependencies depend : fastdep.exe $(SRC) @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c cc -O -o $@ $< sinclude .depend
src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl 0 → 100644 +120 −0 Original line number Diff line number Diff line # arm_serial = Arm armclang compiler, no MPI SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler CC = armclang++ CCFLAGS = -O3 -mcpu=native SHFLAGS = -fPIC DEPFLAGS = -M LINK = armclang++ LINKFLAGS = -g -O LIB = SIZE = size ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings # see possible settings in Section 2.2 (step 4) of manual LMP_INC = -DLAMMPS_GZIP # MPI library # see discussion in Section 2.2 (step 5) of manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = -L../STUBS MPI_LIB = -lmpi_stubs # FFT library # see discussion in Section 2.2 (step 6) of manaul # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW FFT_PATH = -L$(ARMPL_LIBRARIES) FFT_LIB = -larmpl_lp64 # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual # only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC # INC = path(s) for jpeglib.h and/or png.h # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # do not edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) # Path to src files vpath %.cpp .. vpath %.h .. # Link target $(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library targets lib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ $(OBJ) $(EXTRA_LIB) $(LIB) # Compilation rules %.o:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ %.o:%.cu $(EXTRA_CPP_DEPENDS) $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< # Individual dependencies depend : fastdep.exe $(SRC) @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c cc -O -o $@ $< sinclude .depend
