Loading doc/src/Section_start.txt +1 −2 Original line number Diff line number Diff line Loading @@ -455,8 +455,7 @@ and related PPPM operations are somewhat insensitive to floating point truncation errors and thus do not always need to be performed in double precision. Using the -DFFT_SINGLE setting trades off a little accuracy for reduced memory use and parallel communication costs for transposing 3d FFT data. Note that single precision FFTs have only been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. transposing 3d FFT data. Step 7 :h6 Loading doc/src/pair_buck.txt +7 −2 Original line number Diff line number Diff line Loading @@ -120,6 +120,9 @@ cutoff (distance units) cutoff2 (distance units) :ul The second coefficient, rho, must be greater than zero. The coefficients A, rho, and C can be written as analytical expressions of epsilon and sigma, in analogy to the Lennard-Jones potential "(Khrapak)"_#Khrapak. The latter 2 coefficients are optional. If not specified, the global A,C and Coulombic cutoffs are used. If only one cutoff is specified, Loading @@ -127,7 +130,6 @@ it is used as the cutoff for both A,C and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the A,C and Coulombic cutoffs for this type pair. You cannot specify 2 cutoffs for style {buck}, since it has no Coulombic terms. For {buck/coul/long} only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the Loading Loading @@ -194,3 +196,6 @@ only enabled if LAMMPS was built with that package. See the "pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html [Default:] none :link(Khrapak) [(Khrapak)] Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011). lib/voronoi/Install.py 0 → 100644 +116 −0 Original line number Diff line number Diff line #!/usr/bin/env python # install.py tool to download, unpack, build, and link to the Voro++ library # used to automate the steps described in the README file in this dir import sys,os,re,urllib,commands # help message help = """ Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir specify one or more options, order does not matter gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~ -v = version of Voro++ to download and build default = voro++-0.4.6 (current as of Jan 2015) -g = grab (download) from math.lbl.gov/voro++ website unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6) if optional gname specified, rename version dir to gname within gdir -b = build Voro++, bdir = Voro++ home directory note that bdir must include the version suffix unless renamed -l = create 2 softlinks (includelink,liblink) in lib/voronoi to src dir of ldir = Voro++ home directory note that ldir must include the version suffix unless renamed """ # settings version = "voro++-0.4.6" url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # print error message or help def error(str=None): if not str: print help else: print "ERROR",str sys.exit() # expand to full path name # process leading '~' or relative path def fullpath(path): return os.path.abspath(os.path.expanduser(path)) # parse args args = sys.argv[1:] nargs = len(args) if nargs == 0: error() grabflag = 0 buildflag = 0 linkflag = 0 iarg = 0 while iarg < nargs: if args[iarg] == "-v": if iarg+2 > nargs: error() version = args[iarg+1] iarg += 2 elif args[iarg] == "-g": if iarg+2 > nargs: error() grabflag = 1 grabdir = args[iarg+1] grabname = None if iarg+2 < nargs and args[iarg+2][0] != '-': grabname = args[iarg+2] iarg += 1 iarg += 2 elif args[iarg] == "-b": if iarg+2 > nargs: error() buildflag = 1 builddir = args[iarg+1] iarg += 2 elif args[iarg] == "-l": if iarg+2 > nargs: error() linkflag = 1 linkdir = args[iarg+1] iarg += 2 else: error() # download and unpack Voro++ tarball if grabflag: print "Downloading Voro++ ..." grabdir = fullpath(grabdir) if not os.path.isdir(grabdir): error("Grab directory does not exist") urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version)) print "Unpacking Voro++ tarball ..." tardir = "%s/%s" % (grabdir,version) if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir) cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version) txt = commands.getoutput(cmd) print tardir,grabdir,grabname if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname)) # build Voro++ if buildflag: print "Building Voro++ ..." cmd = "cd %s; make" % builddir txt = commands.getoutput(cmd) print txt # create 2 links in lib/voronoi to Voro++ src dir if linkflag: print "Creating links to Voro++ include and lib files" if os.path.isfile("includelink") or os.path.islink("includelink"): os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") cmd = "ln -s %s/src includelink" % linkdir commands.getoutput(cmd) cmd = "ln -s %s/src liblink" % linkdir commands.getoutput(cmd) lib/voronoi/README +2 −2 Original line number Diff line number Diff line Loading @@ -9,8 +9,8 @@ Laboratory. ----------------- You must perform the following steps yourself, or you can use the install.py Python script to automate any or all steps of the process. Type "python install.py" for instructions. Install.py Python script to automate any or all steps of the process. Type "python Install.py" for instructions. 1. Download Voro++ at http://math.lbl.gov/voro++/download either as a tarball or via SVN, and unpack the Loading lib/voronoi/install.pydeleted 100644 → 0 +0 −163 Original line number Diff line number Diff line #!usr/local/python # install.py tool to download, unpack, build, and link to the Voro++ library # used to automate the steps described in the README file in this dir import sys,os,re,urllib,commands help = """ Syntax: install.py -d dir -v version -g -b -i installdir -l incdir libdir specify one or more options, order does not matter -d = dir to download tarball to, unpack tarball in, perform build in dir will be created if it doesn't exist (only last level) default = this dir -v = version of Voro++ to download and work with default = voro++-0.4.6 (current as of Jan 2015) -g = download (grab) tarball from http://math.lbl.gov/voro++/download/dir/version -b = build Voro++ by invoking "make" in its home dir no default -i = install Voro++ by invoking "make install" in its home dir installdir arg is optional: if not specified, installs at PREFIX defined in config.mk file if specified, will overwrite PREFIX and install there if PREFIX starts with /usr, will invoke "sudo make install" -l = create two links to incdir and libdir incdir and libdir are optional (specify neither or both): if specified, includelink and liblink are to those two dirs these are dirs where Voro++ include files and lib file are if not specified and no install, links are to Voro++ src dir if not specified and install performed, links are to include and lib dirs under PREFIX """ def error(): print help sys.exit() # parse args args = sys.argv if len(args) == 1: error() dir = "." version = "voro++-0.4.6" grabflag = 0 buildflag = 0 installflag = 0 linkflag = 0 iarg = 1 while iarg < len(args): if args[iarg] == "-d": if iarg+2 > len(args): error() dir = args[iarg+1] iarg += 2 elif args[iarg] == "-v": if iarg+2 > len(args): error() version = args[iarg+1] iarg += 2 elif args[iarg] == "-g": grabflag = 1 iarg += 1 elif args[iarg] == "-b": buildflag = 1 iarg += 1 elif args[iarg] == "-i": installflag = 1 if iarg+1 == len(args) or args[iarg+1][0] == '-': installdir = "" iarg += 1 else: if iarg+2 > len(args): error() installdir = args[iarg+1] iarg += 2 elif args[iarg] == "-l": linkflag = 1 if iarg+1 == len(args) or args[iarg+1][0] == '-' or \ iarg+2 == len(args) or args[iarg+2][0] == '-': includedir = libdir = "" iarg += 1 else: if iarg+3 > len(args): error() includedir = args[iarg+1] libdir = args[iarg+2] iarg += 3 else: error() dir = os.path.abspath(dir) url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # create dir if does not exist if not os.path.isdir(dir): if os.path.isfile(dir): print "ERROR: Dir already exists as file" sys.exit() os.mkdir(dir) if not os.path.isdir(dir): print "ERROR: Unable to create dir" sys.exit() # download and unpack tarball if grabflag: print "Downloading Voro++ tarball ..." urllib.urlretrieve(url,"%s/%s.tar.gz" % (dir,version)) print "Unpacking Voro++ tarball ..." cmd = "cd %s; tar zxvf %s.tar.gz" % (dir,version) txt = commands.getoutput(cmd) # build Voro++ in its dir if buildflag: print "Building Voro++ ..." cmd = "cd %s/%s; make" % (dir,version) txt = commands.getoutput(cmd) print txt # install Voro++ # if installdir set, overwrite PREFIX var in its config.mk file # if PREFIX var starts with /usr, invoke sudo make install, else make install if installflag: print "Installing Voro++ ..." if installdir: txt = open("%s/%s/config.mk" % (dir,version),'r').read() txt = re.sub("PREFIX=.*?\n","PREFIX=%s\n" % installdir,txt) open("%s/%s/config.mk" % (dir,version),'w').write(txt) print "TXT:",txt txt = open("%s/%s/config.mk" % (dir,version),'r').read() var = re.findall("PREFIX=.*?\n",txt) prefix = var[0].split('=')[1].strip() if prefix.startswith("/usr"): cmd = "cd %s/%s; sudo make install" % (dir,version) else: cmd = "cd %s/%s; make install" % (dir,version) txt = commands.getoutput(cmd) print txt # create links in this dir to Voro++ include and lib files if linkflag: print "Creating links to Voro++ include and lib files" if os.path.isfile("includelink") or os.path.islink("includelink"): os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") if includedir: cmd = "ln -s %s includelink" % includedir txt = commands.getoutput(cmd) cmd = "ln -s %s liblink" % linkdir txt = commands.getoutput(cmd) elif not installflag: cmd = "ln -s %s/%s/src includelink" % (dir,version) txt = commands.getoutput(cmd) cmd = "ln -s %s/%s/src liblink" % (dir,version) txt = commands.getoutput(cmd) else: cmd = "ln -s %s/include includelink" % prefix txt = commands.getoutput(cmd) cmd = "ln -s %s/lib liblink" % prefix txt = commands.getoutput(cmd) Loading
doc/src/Section_start.txt +1 −2 Original line number Diff line number Diff line Loading @@ -455,8 +455,7 @@ and related PPPM operations are somewhat insensitive to floating point truncation errors and thus do not always need to be performed in double precision. Using the -DFFT_SINGLE setting trades off a little accuracy for reduced memory use and parallel communication costs for transposing 3d FFT data. Note that single precision FFTs have only been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. transposing 3d FFT data. Step 7 :h6 Loading
doc/src/pair_buck.txt +7 −2 Original line number Diff line number Diff line Loading @@ -120,6 +120,9 @@ cutoff (distance units) cutoff2 (distance units) :ul The second coefficient, rho, must be greater than zero. The coefficients A, rho, and C can be written as analytical expressions of epsilon and sigma, in analogy to the Lennard-Jones potential "(Khrapak)"_#Khrapak. The latter 2 coefficients are optional. If not specified, the global A,C and Coulombic cutoffs are used. If only one cutoff is specified, Loading @@ -127,7 +130,6 @@ it is used as the cutoff for both A,C and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the A,C and Coulombic cutoffs for this type pair. You cannot specify 2 cutoffs for style {buck}, since it has no Coulombic terms. For {buck/coul/long} only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the Loading Loading @@ -194,3 +196,6 @@ only enabled if LAMMPS was built with that package. See the "pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html [Default:] none :link(Khrapak) [(Khrapak)] Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).
lib/voronoi/Install.py 0 → 100644 +116 −0 Original line number Diff line number Diff line #!/usr/bin/env python # install.py tool to download, unpack, build, and link to the Voro++ library # used to automate the steps described in the README file in this dir import sys,os,re,urllib,commands # help message help = """ Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir specify one or more options, order does not matter gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~ -v = version of Voro++ to download and build default = voro++-0.4.6 (current as of Jan 2015) -g = grab (download) from math.lbl.gov/voro++ website unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6) if optional gname specified, rename version dir to gname within gdir -b = build Voro++, bdir = Voro++ home directory note that bdir must include the version suffix unless renamed -l = create 2 softlinks (includelink,liblink) in lib/voronoi to src dir of ldir = Voro++ home directory note that ldir must include the version suffix unless renamed """ # settings version = "voro++-0.4.6" url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # print error message or help def error(str=None): if not str: print help else: print "ERROR",str sys.exit() # expand to full path name # process leading '~' or relative path def fullpath(path): return os.path.abspath(os.path.expanduser(path)) # parse args args = sys.argv[1:] nargs = len(args) if nargs == 0: error() grabflag = 0 buildflag = 0 linkflag = 0 iarg = 0 while iarg < nargs: if args[iarg] == "-v": if iarg+2 > nargs: error() version = args[iarg+1] iarg += 2 elif args[iarg] == "-g": if iarg+2 > nargs: error() grabflag = 1 grabdir = args[iarg+1] grabname = None if iarg+2 < nargs and args[iarg+2][0] != '-': grabname = args[iarg+2] iarg += 1 iarg += 2 elif args[iarg] == "-b": if iarg+2 > nargs: error() buildflag = 1 builddir = args[iarg+1] iarg += 2 elif args[iarg] == "-l": if iarg+2 > nargs: error() linkflag = 1 linkdir = args[iarg+1] iarg += 2 else: error() # download and unpack Voro++ tarball if grabflag: print "Downloading Voro++ ..." grabdir = fullpath(grabdir) if not os.path.isdir(grabdir): error("Grab directory does not exist") urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version)) print "Unpacking Voro++ tarball ..." tardir = "%s/%s" % (grabdir,version) if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir) cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version) txt = commands.getoutput(cmd) print tardir,grabdir,grabname if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname)) # build Voro++ if buildflag: print "Building Voro++ ..." cmd = "cd %s; make" % builddir txt = commands.getoutput(cmd) print txt # create 2 links in lib/voronoi to Voro++ src dir if linkflag: print "Creating links to Voro++ include and lib files" if os.path.isfile("includelink") or os.path.islink("includelink"): os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") cmd = "ln -s %s/src includelink" % linkdir commands.getoutput(cmd) cmd = "ln -s %s/src liblink" % linkdir commands.getoutput(cmd)
lib/voronoi/README +2 −2 Original line number Diff line number Diff line Loading @@ -9,8 +9,8 @@ Laboratory. ----------------- You must perform the following steps yourself, or you can use the install.py Python script to automate any or all steps of the process. Type "python install.py" for instructions. Install.py Python script to automate any or all steps of the process. Type "python Install.py" for instructions. 1. Download Voro++ at http://math.lbl.gov/voro++/download either as a tarball or via SVN, and unpack the Loading
lib/voronoi/install.pydeleted 100644 → 0 +0 −163 Original line number Diff line number Diff line #!usr/local/python # install.py tool to download, unpack, build, and link to the Voro++ library # used to automate the steps described in the README file in this dir import sys,os,re,urllib,commands help = """ Syntax: install.py -d dir -v version -g -b -i installdir -l incdir libdir specify one or more options, order does not matter -d = dir to download tarball to, unpack tarball in, perform build in dir will be created if it doesn't exist (only last level) default = this dir -v = version of Voro++ to download and work with default = voro++-0.4.6 (current as of Jan 2015) -g = download (grab) tarball from http://math.lbl.gov/voro++/download/dir/version -b = build Voro++ by invoking "make" in its home dir no default -i = install Voro++ by invoking "make install" in its home dir installdir arg is optional: if not specified, installs at PREFIX defined in config.mk file if specified, will overwrite PREFIX and install there if PREFIX starts with /usr, will invoke "sudo make install" -l = create two links to incdir and libdir incdir and libdir are optional (specify neither or both): if specified, includelink and liblink are to those two dirs these are dirs where Voro++ include files and lib file are if not specified and no install, links are to Voro++ src dir if not specified and install performed, links are to include and lib dirs under PREFIX """ def error(): print help sys.exit() # parse args args = sys.argv if len(args) == 1: error() dir = "." version = "voro++-0.4.6" grabflag = 0 buildflag = 0 installflag = 0 linkflag = 0 iarg = 1 while iarg < len(args): if args[iarg] == "-d": if iarg+2 > len(args): error() dir = args[iarg+1] iarg += 2 elif args[iarg] == "-v": if iarg+2 > len(args): error() version = args[iarg+1] iarg += 2 elif args[iarg] == "-g": grabflag = 1 iarg += 1 elif args[iarg] == "-b": buildflag = 1 iarg += 1 elif args[iarg] == "-i": installflag = 1 if iarg+1 == len(args) or args[iarg+1][0] == '-': installdir = "" iarg += 1 else: if iarg+2 > len(args): error() installdir = args[iarg+1] iarg += 2 elif args[iarg] == "-l": linkflag = 1 if iarg+1 == len(args) or args[iarg+1][0] == '-' or \ iarg+2 == len(args) or args[iarg+2][0] == '-': includedir = libdir = "" iarg += 1 else: if iarg+3 > len(args): error() includedir = args[iarg+1] libdir = args[iarg+2] iarg += 3 else: error() dir = os.path.abspath(dir) url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # create dir if does not exist if not os.path.isdir(dir): if os.path.isfile(dir): print "ERROR: Dir already exists as file" sys.exit() os.mkdir(dir) if not os.path.isdir(dir): print "ERROR: Unable to create dir" sys.exit() # download and unpack tarball if grabflag: print "Downloading Voro++ tarball ..." urllib.urlretrieve(url,"%s/%s.tar.gz" % (dir,version)) print "Unpacking Voro++ tarball ..." cmd = "cd %s; tar zxvf %s.tar.gz" % (dir,version) txt = commands.getoutput(cmd) # build Voro++ in its dir if buildflag: print "Building Voro++ ..." cmd = "cd %s/%s; make" % (dir,version) txt = commands.getoutput(cmd) print txt # install Voro++ # if installdir set, overwrite PREFIX var in its config.mk file # if PREFIX var starts with /usr, invoke sudo make install, else make install if installflag: print "Installing Voro++ ..." if installdir: txt = open("%s/%s/config.mk" % (dir,version),'r').read() txt = re.sub("PREFIX=.*?\n","PREFIX=%s\n" % installdir,txt) open("%s/%s/config.mk" % (dir,version),'w').write(txt) print "TXT:",txt txt = open("%s/%s/config.mk" % (dir,version),'r').read() var = re.findall("PREFIX=.*?\n",txt) prefix = var[0].split('=')[1].strip() if prefix.startswith("/usr"): cmd = "cd %s/%s; sudo make install" % (dir,version) else: cmd = "cd %s/%s; make install" % (dir,version) txt = commands.getoutput(cmd) print txt # create links in this dir to Voro++ include and lib files if linkflag: print "Creating links to Voro++ include and lib files" if os.path.isfile("includelink") or os.path.islink("includelink"): os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") if includedir: cmd = "ln -s %s includelink" % includedir txt = commands.getoutput(cmd) cmd = "ln -s %s liblink" % linkdir txt = commands.getoutput(cmd) elif not installflag: cmd = "ln -s %s/%s/src includelink" % (dir,version) txt = commands.getoutput(cmd) cmd = "ln -s %s/%s/src liblink" % (dir,version) txt = commands.getoutput(cmd) else: cmd = "ln -s %s/include includelink" % prefix txt = commands.getoutput(cmd) cmd = "ln -s %s/lib liblink" % prefix txt = commands.getoutput(cmd)
