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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
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Axel Kohlmeyer
2014-10-02 11:11:07 -04:00
parent 3a5d4208f3 4d473aa473
commit b3b99122af
14 changed files with 553 additions and 76 deletions
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4
doc/Manual.html
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@ -1,7 +1,7 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="25 Sep 2014 version">
<META NAME="docnumber" CONTENT="30 Sep 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>25 Sep 2014 version
<CENTER><H4>30 Sep 2014 version
</H4></CENTER>
<H4>Version info:
</H4>

4
doc/Manual.txt
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@ -1,6 +1,6 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="25 Sep 2014 version">
<META NAME="docnumber" CONTENT="30 Sep 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -18,7 +18,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
25 Sep 2014 version :c,h4
30 Sep 2014 version :c,h4
Version info: :h4

9
src/MAKE/OPTIONS/Makefile.intel_cpu
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@ -6,13 +6,14 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc -openmp -DLAMMPS_MEMALIGN=64 -no-offload
CCFLAGS = -g -O3 -xHost -fno-alias -ansi-alias -restrict -override-limits
CC = mpiicpc
CCFLAGS = -g -O3 -openmp -DLAMMPS_MEMALIGN=64 -no-offload \
-xHost -fno-alias -ansi-alias -restrict -override-limits
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc -openmp
LINKFLAGS = -g -O3 -xHost
LINK = mpiicpc
LINKFLAGS = -g -O3 -openmp -xHost
LIB =
SIZE = size

9
src/MAKE/OPTIONS/Makefile.intel_phi
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@ -6,15 +6,16 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc -openmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
CC = mpiicpc
MIC_OPT = -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
CCFLAGS = -g -O3 -xHost -fno-alias -ansi-alias -restrict \
CCFLAGS = -g -O3 -openmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
-xHost -fno-alias -ansi-alias -restrict \
-override-limits $(MIC_OPT)
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc -openmp -offload
LINKFLAGS = -g -O3 -xHost
LINK = mpiicpc
LINKFLAGS = -g -O3 -xHost -openmp -offload
LIB =
SIZE = size

110
src/MAKE/OPTIONS/Makefile.omp Executable file
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@ -0,0 +1,110 @@
# omp = USER-OMP package with default MPI compiler, default MPI
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -g -O3 -restrict -fopenmp
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx
LINKFLAGS = -g -O -fopenmp
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 manual
# 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 =
FFT_PATH =
FFT_LIB =
# 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)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)

110
src/MAKE/OPTIONS/Makefile.opt Executable file
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@ -0,0 +1,110 @@
# opt = OPT package with default MPI compiler, default MPI
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -g -O3 -restrict
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 manual
# 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 =
FFT_PATH =
FFT_LIB =
# 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)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)

333
src/Make.py
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@ -1,14 +1,17 @@
#!/usr/bin/python
# Make.py tool for building LAMMPS and its package libs
# Make.py tool for managing packages and their auxiliary libs,
# auto-editing machine Makefiles, and building LAMMPS
# Sytax: Make.py -h (for help)
import sys,os,commands,re,copy
# switch abbrevs
# switch classes = created class for each switch
# lib classes = all auxiliary libs in LAMMPS plus "all"
# extra classes = packages that need extra build options
# setargs = allowed settings
# lib classes = auxiliary package libs
# build classes = used to build with certain packages
# option classes = used for options
# setargs = makefile settings
# actionargs = allowed actions (also lib-dir and machine)
abbrevs = "adhjmoprsv"
@ -17,7 +20,8 @@ switchclasses = ("actions","dir","help","jmake","makefile",
"output","packages","redo","settings","verbose")
libclasses = ("atc","awpmd","colvars","cuda","gpu",
"meam","poems","qmmm","reax")
extraclasses = ("intel","kokkos")
buildclasses = ("cc","intel","kokkos")
optionclasses = ("jpg","png","fft")
setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
actionargs = ("lib-all","file","clean","exe")
@ -26,11 +30,15 @@ actionargs = ("lib-all","file","clean","exe")
# functions
# ----------------------------------------------------------------
# print error str and exit
# if flag = 1, print str and exit
# if flag = 0, print str as warning and do not exit
def error(str):
print "ERROR:",str
sys.exit()
def error(str,flag=1):
if flag:
print "ERROR:",str
sys.exit()
else:
print "WARNING:",str
# store command-line args as sw = dict of key/value
# key = switch letter, value = list of following args
@ -56,7 +64,7 @@ def parse_args(args):
if switch == 'a':
sw[switch] = args[first:]
break
last = first+1
last = first
while last < narg and args[last][0] != '-' and \
args[last] not in actionargs and \
not args[last].startswith("lib-"):
@ -96,7 +104,7 @@ Actions:
can specify zero or more actions in any order
except machine must be last (if used)
each action can appear no more than once
if switches used and machine is only action, prefix by "-a" switch
if switches used and machine is only action, must prefix with "-a" switch
actions happen in order below, indpendent of specified order
some actions depend on installed packages
installed packages = currently installed + result of -p switch
@ -160,12 +168,13 @@ Actions:
self.alist[-1] = "exe"
return machine
# build libraries needed in installed packages
# build one or more auxiliary package libraries
def lib(self,suffix):
if suffix != "all":
print " building library",suffix
exec("%s.build()" % suffix)
str = "%s.build()" % suffix
exec(str)
else:
final = packages.final
for one in packages.lib:
@ -185,27 +194,58 @@ Actions:
if makefile: machine = makefile.machine
else: machine = "auto"
make = MakeReader(machine,1)
# if compiler not explicitly set, examine CC makefile setting
# if mpi, use "mpicxx -show" (for example) to determine underlying compiler
if not cc.compiler:
ccfile = make.getvar("CC")
if "mpi" in ccfile[0]:
showtxt = commands.getoutput("%s -show" % ccfile[0])
words = showtxt.split()
if words[0] == "g++" or words[0] == "c++": cc.compiler = "g++"
elif words[0] == "icc": cc.compiler = "icc"
else: cc.compiler = "mpi"
elif "icc" in ccfile: cc.compiler = "icc"
elif "g++" in ccfile: cc.compiler = "g++"
elif "nvcc" in ccfile: cc.compiler = "nvcc"
if cc.compiler == "mpi":
error("Makefile.auto using compiler = mpi, b/c could not grok " +
"%s result from %s -show" % (words[0],ccfile[0]),0)
# be careful to match makefile settings to compiler being used
if tweak:
final = packages.final
if final["opt"]:
if cc.compiler == "icc": make.addvar("CCFLAGS","-restrict")
if final["user-omp"]:
make.addvar("CCFLAGS","-fopenmp")
make.addvar("CCFLAGS","-restrict")
make.addvar("LINKFLAGS","-fopenmp")
if cc.compiler == "icc": make.addvar("CCFLAGS","-restrict")
# KOKKOS Cuda build will add -Xcompiler -fopenmp
if cc.compiler != "nvcc": make.addvar("CCFLAGS","-fopenmp")
if cc.compiler != "nvcc": make.addvar("LINKFLAGS","-fopenmp")
if final["user-intel"]:
if intel.mode == "cpu":
if cc.compiler != "icc":
error("Makefile.auto for intel/cpu but without some settings " +
"b/c may not be using Intel icc compiler",0)
make.addvar("CCFLAGS","-fopenmp")
make.addvar("CCFLAGS","-DLAMMPS_MEMALIGN=64")
make.addvar("CCFLAGS","-restrict")
make.addvar("CCFLAGS","-xHost")
make.addvar("CCFLAGS","-fno-alias")
make.addvar("CCFLAGS","-ansi-alias")
make.addvar("CCFLAGS","-override-limits")
make.addvar("LINKFLAGS","-fopenmp")
make.addvar("CCFLAGS","-DLAMMPS_MEMALIGN=64")
if cc.compiler == "icc": make.addvar("CCFLAGS","-restrict")
make.addvar("CCFLAGS","-xHost")
if cc.compiler == "icc": make.addvar("CCFLAGS","-fno-alias")
if cc.compiler == "icc": make.addvar("CCFLAGS","-ansi-alias")
if cc.compiler == "icc": make.addvar("CCFLAGS","-override-limits")
if cc.compiler == "icc": make.addvar("LINKFLAGS","-xHost")
make.delvar("CCFLAGS","-DLMP_INTEL_OFFLOAD")
make.delvar("LINKFLAGS","-offload")
elif intel.mode == "phi":
if cc.compiler != "icc":
error("Makefile.auto for intel/phi but may not be " +
"using Intel icc compiler",0)
make.addvar("CCFLAGS","-fopenmp")
make.addvar("CCFLAGS","-DLAMMPS_MEMALIGN=64")
make.addvar("CCFLAGS","-restrict")
@ -227,6 +267,9 @@ Actions:
make.delvar("CUDA")
make.delvar("MIC")
elif kokkos.mode == "cuda":
if cc.compiler != "nvcc":
error("Makefile.auto for kokkos/cuda but may not be " +
"using NVIDIA nvcc compiler",0)
make.addvar("OMP","yes")
make.addvar("CUDA","yes")
make.delvar("MIC")
@ -258,6 +301,49 @@ Actions:
make.delvar("LMP_INC","-DLAMMPS_BIGBIG")
make.addvar("LMP_INC","-DLAMMPS_SMALLSMALL")
if jpg:
if jpg.on == 0:
make.delvar("LMP_INC","-DLAMMPS_JPEG")
make.delvar("JPG_LIB","-ljpeg")
else:
make.addvar("LMP_INC","-DLAMMPS_JPEG")
make.addvar("JPG_LIB","-ljpeg")
if jpg.dir:
make.addvar("JPG_INC","-I%s/include" % jpg.dir)
make.addvar("JPG_PATH","-L%s/lib" % jpg.dir)
else:
if jpg.incdir: make.addvar("JPG_INC","-I%s" % jpg.incdir)
if jpg.libdir: make.addvar("JPG_PATH","-L%s" % jpg.libdir)
if png:
if png.on == 0:
make.delvar("LMP_INC","-DLAMMPS_PNG")
make.delvar("JPG_LIB","-lpng")
else:
make.addvar("LMP_INC","-DLAMMPS_PNG")
make.addvar("JPG_LIB","-lpng")
if png.dir:
make.addvar("JPG_INC","-I%s/include" % png.dir)
make.addvar("JPG_PATH","-L%s/lib" % png.dir)
else:
if png.incdir: make.addvar("JPG_INC","-I%s" % png.incdir)
if png.libdir: make.addvar("JPG_PATH","-L%s" % png.libdir)
if fft:
make.delvar("FFT_INC","*")
make.delvar("FFT_PATH","*")
make.delvar("FFT_LIB","*")
if fft.mode == "none": make.addvar("FFT_INC","-DFFT_NONE")
else:
make.addvar("FFT_INC","-DFFT_%s" % fft.mode.upper())
make.addvar("FFT_LIB",fft.lib)
if fft.dir:
make.addvar("FFT_INC","-I%s/include" % fft.dir)
make.addvar("FFT_PATH","-L%s/lib" % fft.dir)
else:
if fft.incdir: make.addvar("FFT_INC","-I%s" % fft.incdir)
if fft.libdir: make.addvar("FFT_PATH","-L%s" % fft.libdir)
make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
print "Created src/MAKE/MINE/Makefile.auto"
@ -281,7 +367,7 @@ Actions:
if not os.path.isfile("%s/lmp_auto" % dir.src):
if not verbose: print txt
error('Unsuccessful "make auto"')
else: print "Created src/lmp_auto"
elif not output: print "Created src/lmp_auto"
# dir switch
@ -335,11 +421,12 @@ Syntax: Make.py switch args ... {action1} {action2} ...
switches for libs:
-atc, -awpmd, -colvars, -cuda
-gpu, -meam, -poems, -qmmm, -reax
switches for extra package options:
-intel, -kokkos
switches for build and makefile options:
-intel, -kokkos, -jpg, -png, -fft
add -h switch to command line to print this message
and help on other specified switches or actions
add -a switch if not seeing action help
"""
# jmake switch
@ -420,9 +507,9 @@ class Packages:
lib = all standard and user packages with auxiliary libs
can abbreviate package names and yes/no
omp = user-omp = yes-user-omp
#omp = #user-omp = no-user-omp
user = yes-user, #user = no-user
all = yes-all, #all = no-all
^omp = ^user-omp = no-user-omp
user = yes-user, ^user = no-user
all = yes-all, ^all = no-all
when action performed, list is processed in order,
as if typed "make yes/no" for each
if "orig" or "original" is last package in list,
@ -455,17 +542,17 @@ class Packages:
plist.append("yes-%s" % one)
elif "user-"+one in user:
plist.append("yes-user-%s" % one)
elif one == '#' and one[1:] in std:
elif one == '^' and one[1:] in std:
plist.append("no-%s" % one[1:])
elif one[0] == '#' and one[1:] in user:
elif one[0] == '^' and one[1:] in user:
plist.append("no-%s" % one[1:])
elif one[0] == '#' and "user-"+one[1:] in user:
elif one[0] == '^' and "user-"+one[1:] in user:
plist.append("no-user-%s" % one[1:])
elif one == "std" or one == "standard" or one == "user" or \
one == "lib" or one == "all":
plist.append("yes-%s" % one)
elif one == "#std" or one == "#standard" or one == "#user" or \
one == "#lib" or one == "#all":
elif one == "^std" or one == "^standard" or one == "^user" or \
one == "^lib" or one == "^all":
plist.append("no-%s" % one[1:])
elif one == "orig": plist.append(one)
else: error("Invalid package name %s" % one)
@ -1115,9 +1202,30 @@ class REAX:
else: print "Created lib/reax library"
# ----------------------------------------------------------------
# extra classes for intel and kokkos package options
# classes for cc and intel and kokkos build options
# ----------------------------------------------------------------
# Cc class
class Cc:
def __init__(self,list):
if list == None: self.inlist = None
else: self.inlist = list[:]
self.compiler = ""
def help(self):
return """
-cc compiler
compiler = g++ or icc or nvcc
def = CC setting in Makefile.auto, result of "mpicxx -show" if MPI wrapper
used to tailor some Makefile.machine settings for specific compilers
"""
def check(self):
if self.inlist == None: return
if len(self.inlist) != 1: error("-cc args are invalid")
self.compiler = self.inlist[0]
# Intel class
class Intel:
@ -1174,6 +1282,120 @@ class Kokkos:
self.arch = words[1]
self.archflag = 1
else: error("-kokkos args are invalid")
# ----------------------------------------------------------------
# classes for JPG, PNG, FFT makefile options
# ----------------------------------------------------------------
# Jpg class
class Jpg:
def __init__(self,list):
self.inlist = list[:]
self.on = 1
self.dir = self.incdir = self.libdir = ""
def help(self):
return """
-jpg flag dir=homedir idir=incdir ldir=libdir
all args are optional, flag must come first if specified
flag = yes or no (def = yes)
include or exclude JPEG support
adds/removes -DLAMMPS_JPEG and -ljpeg settings
dir = home dir for include and library files (def = none)
adds -Idir/include and -Ldir/lib settings
if set, overrides idir and ldir args
idir = dir for include file (def = none)
adds -Iidir setting
ldir = dir for library file (def = none)
adds -Lldir setting
"""
def check(self):
for i,one in enumerate(self.inlist):
if one == "no" and i == 0: self.on = 0
elif one == "yes" and i == 0: self.on = 1
else:
words = one.split('=')
if len(words) != 2: error("-jpeg args are invalid")
if words[0] == "dir": self.dir = words[1]
elif words[0] == "idir": self.incdir = words[1]
elif words[0] == "ldir": self.libdir = words[1]
else: error("-jpeg args are invalid")
# Png class
class Png:
def __init__(self,list):
self.inlist = list[:]
self.on = 1
self.dir = self.incdir = self.libdir = ""
def help(self):
return """
-png flag dir=homedir idir=incdir ldir=libdir
all args are optional, flag must come first if specified
flag = yes or no (def = yes)
include or exclude PNG support
adds/removes -DLAMMPS_PNG and -lpng settings
dir = home dir for include and library files (def = none)
adds -Idir/include and -Ldir/lib settings
if set, overrides idir and ldir args
idir = dir for include file (def = none)
adds -Iidir setting
ldir = dir for library file (def = none)
adds -Lldir setting
"""
def check(self):
for i,one in enumerate(self.inlist):
if one == "no" and i == 0: self.on = 0
elif one == "yes" and i == 0: self.on = 1
else:
words = one.split('=')
if len(words) != 2: error("-png args are invalid")
if words[0] == "dir": self.dir = words[1]
elif words[0] == "idir": self.incdir = words[1]
elif words[0] == "ldir": self.libdir = words[1]
else: error("-png args are invalid")
# Fft class
class Fft:
def __init__(self,list):
self.inlist = list[:]
self.dir = self.incdir = self.libdir = ""
def help(self):
return """
-fft mode lib=libname dir=homedir idir=incdir ldir=libdir
mode is required, all other args are optional
removes all current FFT variable settings
mode = none or fftw or ...
adds -DFFT_MODE setting
lib = name of FFT library to link with (def is libname = mode)
adds -lliblibname setting
dir = home dir for include and library files (def = none)
adds -Idir/include and -Ldir/lib settings
if set, overrides idir and ldir args
idir = dir for include file (def = none)
adds -Iidir setting
ldir = dir for library file (def = none)
adds -Lldir setting
"""
def check(self):
if not len(self.inlist): error("-fft args are invalid")
self.mode = self.inlist[0]
self.lib = "-l%s" % self.mode
for one in self.inlist[1:]:
words = one.split('=')
if len(words) != 2: error("-fft args are invalid")
if words[0] == "lib": self.lib = "-l%s" % words[1]
elif words[0] == "dir": self.dir = words[1]
elif words[0] == "idir": self.incdir = words[1]
elif words[0] == "ldir": self.libdir = words[1]
else: error("-fft args are invalid")
# ----------------------------------------------------------------
# auxiliary classes
@ -1344,6 +1566,11 @@ class MakeReader:
cmd_switches,cmd_switch_order = parse_args(sys.argv[1:])
if "v" in cmd_switches:
print "Command-line parsing:"
for switch in cmd_switch_order:
print " %s: %s" % (switch,' '.join(cmd_switches[switch]))
# check for redo switch, process redo file
# redolist = list of commands to execute
@ -1411,8 +1638,9 @@ while 1:
for one in switchclasses: exec("%s = None" % one)
for one in libclasses: exec("%s = None" % one)
for one in extraclasses: exec("%s = None" % one)
for one in buildclasses: exec("%s = None" % one)
for one in optionclasses: exec("%s = None" % one)
# classes = dictionary of created classes
# key = switch, value = class instance
@ -1424,16 +1652,22 @@ while 1:
txt = '%s = classes["%s"] = %s(switches["%s"])' % \
(switchclasses[i],switch,capitalized,switch)
exec(txt)
elif len(switch) > 1 and switch in libclasses:
elif switch in libclasses:
i = libclasses.index(switch)
txt = '%s = classes["%s"] = %s(switches["%s"])' % \
(libclasses[i],switch,libclasses[i].upper(),switch)
exec(txt)
elif len(switch) > 1 and switch in extraclasses:
i = extraclasses.index(switch)
capitalized = extraclasses[i][0].upper() + extraclasses[i][1:]
elif switch in buildclasses:
i = buildclasses.index(switch)
capitalized = buildclasses[i][0].upper() + buildclasses[i][1:]
txt = '%s = classes["%s"] = %s(switches["%s"])' % \
(extraclasses[i],switch,capitalized,switch)
(buildclasses[i],switch,capitalized,switch)
exec(txt)
elif switch in optionclasses:
i = optionclasses.index(switch)
capitalized = optionclasses[i][0].upper() + optionclasses[i][1:]
txt = '%s = classes["%s"] = %s(switches["%s"])' % \
(optionclasses[i],switch,capitalized,switch)
exec(txt)
else: error("Unknown command-line switch -%s" % switch)
@ -1448,7 +1682,7 @@ while 1:
sys.exit()
# create needed default classes if not specified with switch
# dir and packages, all lib classes so defaults are set
# dir and packages plus lib and build classes so defaults are set
if not dir: dir = Dir(None)
if not packages: packages = Packages(None)
@ -1457,7 +1691,7 @@ while 1:
txt = "if not %s: %s = %s(None)" % (one,one,one.upper())
exec(txt)
for one in extraclasses:
for one in buildclasses:
capitalized = one[0].upper() + one[1:]
txt = "if not %s: %s = %s(None)" % (one,one,capitalized)
exec(txt)
@ -1468,7 +1702,7 @@ while 1:
# prep for action
# actions.setup() detects if last action = machine
# if yes, induces addition of "-m" and "-o" switches
# if yes, induce addition of "-m" and "-o" switches
dir.setup()
packages.setup()
@ -1480,13 +1714,13 @@ while 1:
if 'm' not in switches:
switches['m'] = [machine]
switch_order.insert(-1,'m')
classes['m'] = Makefile(switches['m'])
classes['m'].check()
makefile = classes['m'] = Makefile(switches['m'])
makefile.check()
if 'o' not in switches:
switches['o'] = [machine]
switch_order.insert(-1,'o')
classes['o'] = Makefile(switches['o'])
classes['o'].check()
output = classes['o'] = Makefile(switches['o'])
output.check()
# perform actions
@ -1507,7 +1741,8 @@ while 1:
if output and actions and "exe" in actions.alist:
txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
commands.getoutput(txt)
print "Created lmp_%s in %s" % (output.machine,dir.cwd)
# write current Make.py command to src/Make.py.last
argstr = switch2str(switches,switch_order)

8
src/USER-CUDA/Install.sh
View File

@ -153,10 +153,10 @@ action pair_tersoff_cuda.cpp pair_tersoff.cpp
action pair_tersoff_cuda.h pair_tersoff.cpp
action pair_tersoff_zbl_cuda.cpp pair_tersoff_zbl.cpp
action pair_tersoff_zbl_cuda.h pair_tersoff_zbl.cpp
action pppm_cuda.cpp
action pppm_cuda.h
action pppm_old.cpp
action pppm_old.h
action pppm_cuda.cpp pppm.cpp
action pppm_cuda.h pppm.cpp
action pppm_old.cpp pppm.cpp
action pppm_old.h pppm.cpp
action verlet_cuda.cpp
action verlet_cuda.h

1
src/compute.cpp
View File

@ -75,6 +75,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
invoked_scalar = invoked_vector = invoked_array = -1;
invoked_peratom = invoked_local = -1;
invoked_flag = 0;
// set modify defaults

18
src/dump_custom.cpp
View File

@ -402,13 +402,23 @@ int DumpCustom::count()
}
// invoke Computes for per-atom quantities
// only if within a run or minimize
// else require that computes are current
// this prevents a compute from being invoked by the WriteDump class
if (ncompute) {
for (i = 0; i < ncompute; i++)
if (!(compute[i]->invoked_flag & INVOKED_PERATOM)) {
compute[i]->compute_peratom();
compute[i]->invoked_flag |= INVOKED_PERATOM;
if (update->whichflag == 0) {
for (i = 0; i < ncompute; i++)
if (compute[i]->invoked_peratom != update->ntimestep)
error->all(FLERR,"Compute used in dump between runs is not current");
} else {
for (i = 0; i < ncompute; i++) {
if (!(compute[i]->invoked_flag & INVOKED_PERATOM)) {
compute[i]->compute_peratom();
compute[i]->invoked_flag |= INVOKED_PERATOM;
}
}
}
}
// evaluate atom-style Variables for per-atom quantities

17
src/dump_local.cpp
View File

@ -231,12 +231,21 @@ int DumpLocal::count()
int i;
// invoke Computes for local quantities
// only if within a run or minimize
// else require that computes are current
// this prevents a compute from being invoked by the WriteDump class
if (ncompute) {
for (i = 0; i < ncompute; i++) {
if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
compute[i]->compute_local();
compute[i]->invoked_flag |= INVOKED_LOCAL;
if (update->whichflag == 0) {
for (i = 0; i < ncompute; i++)
if (compute[i]->invoked_local != update->ntimestep)
error->all(FLERR,"Compute used in dump between runs is not current");
} else {
for (i = 0; i < ncompute; i++) {
if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
compute[i]->compute_local();
compute[i]->invoked_flag |= INVOKED_LOCAL;
}
}
}
}

1
src/neighbor.cpp
View File

@ -95,6 +95,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
maxhold = 0;
xhold = NULL;
lastcall = -1;
// binning

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "25 Sep 2014"
#define LAMMPS_VERSION "30 Sep 2014"

3
src/write_dump.cpp
View File

@ -88,6 +88,5 @@ void WriteDump::command(int narg, char **arg)
// delete the Dump instance and local storage
delete dump;
delete[] dumpargs;
delete [] dumpargs;
}