forked from lijiext/lammps
Merge pull request #993 from lammps/doc-plus-makefile
better rRESPA doc page, also a new Makefile.theta
This commit is contained in:
Steve Plimpton
GitHub
commit
f288331874
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@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the
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iterations of level 2 per iteration of level 3, etc. N-1 looping
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parameters must be specified.
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The "timestep"_timestep.html command sets the timestep for the
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outermost rRESPA level. Thus if the example command above for a
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4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
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would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that
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specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html
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parameters, "dump"_dump.html every N timesteps, etc) refer to the
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outermost timesteps.
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Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
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you could choose to have bond interactions computed 8x per large
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timestep, angle interactions computed 4x, pair interactions computed
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2x, and long-range interactions once per large timestep.
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The "timestep"_timestep.html command sets the large timestep for the
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outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for
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4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
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inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS
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commands that specify number of timesteps (e.g. "thermo"_thermo.html
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for thermo output every N steps, "neigh_modify
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delay/every"_neigh_modify.html parameters, "dump"_dump.html every N
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steps, etc) refer to the outermost timesteps.
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The rRESPA keywords enable you to specify at what level of the
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hierarchy various forces will be computed. If not specified, the
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@ -238,12 +244,24 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a
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For non-biomolecular simulations, the {respa} style can be
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advantageous if there is a clear separation of time scales - fast and
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slow modes in the simulation. Even a LJ system can benefit from
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rRESPA if the interactions are divided by the inner, middle and outer
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keywords. A 2-fold or more speedup can be obtained while maintaining
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good energy conservation. In real units, for a pure LJ fluid at
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liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
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Kcal/mol, the following settings seem to work well:
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slow modes in the simulation. For example, a system of slowly-moving
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charged polymer chains could be setup as follows:
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timestep 4.0
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run_style respa 2 8 :pre
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This is two-level rRESPA with an 8x difference between the short and
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long timesteps. The bonds, angles, dihedrals will be computed every
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0.5 fs (assuming real units), while the pair and kspace interactions
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will be computed once every 4 fs. These are the default settings for
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each kind of interaction, so no additional keywords are necessary.
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Even a LJ system can benefit from rRESPA if the interactions are
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divided by the inner, middle and outer keywords. A 2-fold or more
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speedup can be obtained while maintaining good energy conservation.
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In real units, for a pure LJ fluid at liquid density, with a sigma of
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3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings
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seem to work well:
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timestep 36.0
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run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
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@ -271,9 +289,9 @@ more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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The {verlet/split} style can only be used if LAMMPS was built with the
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REPLICA package. Correspondingly the {respa/omp} style is available only
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if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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REPLICA package. Correspondingly the {respa/omp} style is available
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only if the USER-OMP package was included. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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Whenever using rRESPA, the user should experiment with trade-offs in
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speed and accuracy for their system, and verify that they are
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@ -287,6 +305,17 @@ conserving energy to adequate precision.
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run_style verlet :pre
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For run_style respa, the default assignment of interactions
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to rRESPA levels is as follows:
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bond forces = level 1 (innermost loop)
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angle forces = same level as bond forces
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dihedral forces = same level as angle forces
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improper forces = same level as dihedral forces
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pair forces = leven N (outermost level)
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kspace forces = same level as pair forces
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inner, middle, outer forces = no default :ul
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:line
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:link(Tuckerman3)
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@ -0,0 +1,133 @@
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# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
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# module load perftools-base perftools
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# make theta -j 8
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# pat_build -g mpi -u ./lmp_theta
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SHELL = /bin/sh
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# ---------------------------------------------------------------------
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# compiler/linker settings
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# specify flags and libraries needed for your compiler
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CC = CC -mkl
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#OPTFLAGS = -O0
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OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
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CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
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-fno-alias -ansi-alias -restrict $(OPTFLAGS)
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#CCFLAGS += -DLMP_INTEL_NO_TBB
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#CCFLAGS += -DLAMMPS_BIGBIG
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#CCFLAGS += -D_USE_PAPI
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#CCFLAGS += -D_USE_CRAYPAT_API
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SHFLAGS = -fPIC
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DEPFLAGS = -M
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LINK = $(CC)
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LINKFLAGS = -g -qopenmp $(OPTFLAGS)
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LINKFLAGS += -dynamic
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LIB =
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#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
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LIB += -ltbbmalloc
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#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
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SIZE = size
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ARCHIVE = ar
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ARFLAGS = -rc
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SHLIBFLAGS = -shared
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# ---------------------------------------------------------------------
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# LAMMPS-specific settings, all OPTIONAL
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# specify settings for LAMMPS features you will use
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# if you change any -D setting, do full re-compile after "make clean"
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# LAMMPS ifdef settings
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# see possible settings in Section 2.2 (step 4) of manual
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LMP_INC = -DLAMMPS_GZIP #-DLAMMPS_JPEG
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# MPI library
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# see discussion in Section 2.2 (step 5) of manual
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# MPI wrapper compiler/linker can provide this info
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# can point to dummy MPI library in src/STUBS as in Makefile.serial
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# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
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# INC = path for mpi.h, MPI compiler settings
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# PATH = path for MPI library
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# LIB = name of MPI library
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MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
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MPI_PATH =
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MPI_LIB =
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# FFT library
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# see discussion in Section 2.2 (step 6) of manaul
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# can be left blank to use provided KISS FFT library
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# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
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# PATH = path for FFT library
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# LIB = name of FFT library
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FFT_INC = -DFFT_MKL -DFFT_SINGLE
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FFT_PATH =
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FFT_LIB = -L$(MKLROOT)/lib/intel64/ -Wl,--start-group -lmkl_intel_ilp64 \
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-lmkl_intel_thread -lmkl_core -Wl,--end-group
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# JPEG and/or PNG library
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# see discussion in Section 2.2 (step 7) of manual
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# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
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# INC = path(s) for jpeglib.h and/or png.h
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# PATH = path(s) for JPEG library and/or PNG library
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# LIB = name(s) of JPEG library and/or PNG library
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JPG_INC =
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JPG_PATH =
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JPG_LIB =
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# ---------------------------------------------------------------------
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# build rules and dependencies
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# do not edit this section
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include Makefile.package.settings
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include Makefile.package
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EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
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EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
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EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
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# Path to src files
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vpath %.cpp ..
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vpath %.h ..
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# Link target
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$(EXE): $(OBJ)
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$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
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$(SIZE) $(EXE)
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# Library targets
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lib: $(OBJ)
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$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
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shlib: $(OBJ)
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$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
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$(OBJ) $(EXTRA_LIB) $(LIB)
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# Compilation rules
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%.o:%.cpp
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$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
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%.d:%.cpp
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$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
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%.o:%.cu
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$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
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# Individual dependencies
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depend : fastdep.exe $(SRC)
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@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
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fastdep.exe: ../DEPEND/fastdep.c
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icc -O -o $@ $<
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sinclude .depend
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