forked from lijiext/lammps
convert to KSspace style rather than fix
This commit is contained in:
Steven J. Plimpton
parent
6cfdcd1000
commit
e7f4e059cf
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@ -5,17 +5,32 @@ atom_style full
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read_data data.NaCl
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velocity all set 0.0 0.0 0.0 mom no
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replicate 8 8 8
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pair_style zero 1.0
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pair_coeff * *
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velocity all create 1.5 49893
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neighbor 1.0 bin
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neigh_modify delay 0
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# using the fmm solver with a tolerance in energy of 10^-3
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fix 1 all scafacos fmm tolerance energy 0.001
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fix 1 all nve
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# LAMMPS computes pairwise and long-range Coulombics
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#pair_style coul/long 3.0
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#pair_coeff * *
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#kspace_style pppm 1.0e-3
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# Scafacos computes entire long-range Coulombics
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# use dummy pair style to perform atom sorting
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pair_style zero 1.0
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pair_coeff * *
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#fix 2 all scafacos p3m tolerance field 0.001
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kspace_style scafacos p3m tolerance field 0.001
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timestep 0.005
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thermo 10
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run 100
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@ -0,0 +1,168 @@
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#!/usr/bin/env python
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# Install.py tool to download, unpack, build, and link to the Scafacos library
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# used to automate the steps described in the README file in this dir
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from __future__ import print_function
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import sys,os,re,subprocess
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# help message
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help = """
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Syntax from src dir: make lib-scafacos args="-b"
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or: make lib-scafacos args="-p /usr/local/scafacos"
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Syntax from lib dir: python Install.py -b
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or: python Install.py -p /usr/local/scafacos
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specify zero or more options, order does not matter
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-b = download and build the Scafacos library
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-p = specify folder of existing Scafacos installation
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always creates includelink, liblink to Scafacos dirs
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Example:
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make lib-scafacos args="-b" # download/build in lib/scafacos/scafacos
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make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation in $HOME
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"""
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# settings
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#version = "voro++-0.4.6"
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#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
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# print error message or help
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def error(str=None):
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if not str: print(help)
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else: print("ERROR",str)
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sys.exit()
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# expand to full path name
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# process leading '~' or relative path
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def fullpath(path):
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return os.path.abspath(os.path.expanduser(path))
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def which(program):
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def is_exe(fpath):
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return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
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fpath, fname = os.path.split(program)
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if fpath:
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if is_exe(program):
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return program
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else:
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for path in os.environ["PATH"].split(os.pathsep):
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path = path.strip('"')
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exe_file = os.path.join(path, program)
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if is_exe(exe_file):
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return exe_file
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return None
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def geturl(url,fname):
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success = False
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if which('curl') != None:
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cmd = 'curl -L -o "%s" %s' % (fname,url)
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try:
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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success = True
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except subprocess.CalledProcessError as e:
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print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
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if not success and which('wget') != None:
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cmd = 'wget -O "%s" %s' % (fname,url)
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try:
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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success = True
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except subprocess.CalledProcessError as e:
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print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
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if not success:
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error("Failed to download source code with 'curl' or 'wget'")
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return
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# parse args
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args = sys.argv[1:]
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nargs = len(args)
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#if nargs == 0: error()
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homepath = "."
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buildflag = False
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pathflag = False
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linkflag = True
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iarg = 0
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while iarg < nargs:
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if args[iarg] == "-v":
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if iarg+2 > nargs: error()
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version = args[iarg+1]
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iarg += 2
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elif args[iarg] == "-p":
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if iarg+2 > nargs: error()
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scafacospath = fullpath(args[iarg+1])
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pathflag = True
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iarg += 2
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elif args[iarg] == "-b":
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buildflag = True
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iarg += 1
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else: error()
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homepath = fullpath(homepath)
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#homedir = "%s/%s" % (homepath,version)
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homedir = homepath
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if (pathflag):
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if not os.path.isdir(scafacospath): error("Scafacos path does not exist")
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homedir =scafacospath
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if (buildflag and pathflag):
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error("Cannot use -b and -p flag at the same time")
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#if (not buildflag and not pathflag):
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# error("Have to use either -b or -p flag")
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# download and unpack Scafacos tarball
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if buildflag:
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print("Downloading Scafacos ...")
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geturl(url,"%s/%s.tar.gz" % (homepath,version))
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print("Unpacking Voro++ tarball ...")
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if os.path.exists("%s/%s" % (homepath,version)):
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cmd = 'rm -rf "%s/%s"' % (homepath,version)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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os.remove("%s/%s.tar.gz" % (homepath,version))
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if os.path.basename(homedir) != version:
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if os.path.exists(homedir):
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cmd = 'rm -rf "%s"' % homedir
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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os.rename("%s/%s" % (homepath,version),homedir)
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# build Scafacos
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if buildflag:
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print("Building Scafacos ...")
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cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir
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txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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print(txt.decode('UTF-8'))
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# create 2 links in lib/scafacos to Scafacos include/lib dirs
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if linkflag:
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print("Creating links to Scafacos include and lib files")
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if os.path.isfile("includelink") or os.path.islink("includelink"):
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os.remove("includelink")
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if os.path.isfile("liblink") or os.path.islink("liblink"):
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os.remove("liblink")
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cmd = 'ln -s "scafacos/include" includelink'
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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cmd = 'ln -s "scafacos/lib" liblink'
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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@ -62,8 +62,8 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
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user-intel user-lb user-manifold user-meamc user-meso \
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user-mgpt user-misc user-mofff user-molfile \
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user-netcdf user-omp user-phonon user-qmmm user-qtb \
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user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
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user-uef user-vtk
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user-quip user-reaxc user-scafacos user-smd user-smtbq \
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user-sph user-tally user-uef user-vtk
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PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
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python reax voronoi \
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@ -37,31 +37,18 @@ done
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if (test $1 = 1) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
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sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
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sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package
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sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package
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#sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package
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sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
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# multiline form needed for BSD sed on Macs
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sed -i -e '4 i \
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include ..\/..\/lib\/scafacos\/Makefile.lammps
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' ../Makefile.package.settings
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sed -i -e 's%^PKG_LIB =[ \t]*%&`grep Libs: ../../lib/scafacos/liblink/pkgconfig/scafacos.pc | cut -d " " -f 2-` %' ../Makefile.package
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fi
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elif (test $1 = 0) then
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if (test -e ../Makefile.package) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
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sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
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fi
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fi
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@ -17,6 +17,7 @@
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#include <cstdio>
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#include <cstring>
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#include <cstdlib>
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#include "fix_scafacos.h"
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#include "atom.h"
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#include "comm.h"
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@ -81,7 +82,7 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
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else
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error->all(FLERR,"Illegal fix scafacos command");
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++arg_index;
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tolerance_value = atof(arg[arg_index]);
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tolerance_value = atof(arg[arg_index]);
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++arg_index;
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}
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else
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@ -439,6 +440,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
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{
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if (result)
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{
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printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
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std::string err_msg;
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std::stringstream ss;
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@ -446,8 +448,9 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
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<< fcs_result_get_message(result) << "\n";
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err_msg = ss.str();
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error->one(FLERR, err_msg.c_str());
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error -> all(FLERR, err_msg.c_str());
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fcs_result_destroy(result);
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}
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return true;
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}
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@ -111,4 +111,54 @@ class FixScafacos : public Fix {
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/* ERROR/WARNING messages:
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E: Must use units metal with fix latte command
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UNDOCUMENTED
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E: Fix latte currently runs only in serial
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UNDOCUMENTED
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E: LAMMPS is linked against incompatible LATTE library
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UNDOCUMENTED
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
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UNDOCUMENTED
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E: Could not find fix latte compute ID
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UNDOCUMENTED
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E: Fix latte compute ID does not compute pe/atom
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UNDOCUMENTED
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E: Fix latte requires 3d problem
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UNDOCUMENTED
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E: Fix latte cannot compute Coulomb potential
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UNDOCUMENTED
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E: Fix latte requires 3d simulation
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UNDOCUMENTED
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W: Fix latte should come after all other integration fixes
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UNDOCUMENTED
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E: Internal LATTE problem
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UNDOCUMENTED
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*/
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@ -0,0 +1,308 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Rene Halver (JSC)
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------------------------------------------------------------------------- */
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#include <cstdio>
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#include <cstring>
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#include <cstdlib>
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#include "scafacos.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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// ScaFaCoS library
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#include <string>
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#include <sstream>
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#include "fcs.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
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{
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if (narg < 2) error->all(FLERR,"Illegal scafacos command");
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int n = strlen(arg[0]) + 1;
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method = new char[n];
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strcpy(method,arg[0]);
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// additional args
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int tflag = 0;
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"tolerance") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command");
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tflag = 1;
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if (strcmp(arg[iarg+1],"energy") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
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else if (strcmp(arg[iarg+1],"energy_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
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else if (strcmp(arg[iarg+1],"field") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
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else if (strcmp(arg[iarg+1],"field_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
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else if (strcmp(arg[iarg+1],"potential") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
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else if (strcmp(arg[iarg+1],"potential_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
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else error->all(FLERR,"Illegal scafacos command");
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tolerance = force->numeric(FLERR,arg[iarg+2]);
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iarg += 3;
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} else error->all(FLERR,"Illegal scafacos command");
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}
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if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command");
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// initializations
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me = comm->me;
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initialized = 0;
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maxatom = 0;
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epot = NULL;
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efield = NULL;
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}
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/* ---------------------------------------------------------------------- */
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Scafacos::~Scafacos()
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{
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delete [] method;
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memory->destroy(epot);
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memory->destroy(efield);
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// NOTE: any clean-up call to ScaFaCoS needed?
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}
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/* ---------------------------------------------------------------------- */
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void Scafacos::init()
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{
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// error checks
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// NOTE: allow triclinic at some point
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if (domain->dimension == 2)
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error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
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if (domain->triclinic)
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error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
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// one-time initialization of ScaFaCoS
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||||
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if (!initialized) {
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result = fcs_init(&fcs,method,world);
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check_result(result);
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setup_handle();
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result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
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check_result(result);
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|
||||
if (me == 0) fcs_print_parameters(fcs);
|
||||
|
||||
double **x = atom->x;
|
||||
double *q = atom->q;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
result = fcs_tune(fcs,nlocal,&x[0][0],q);
|
||||
}
|
||||
|
||||
initialized = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Scafacos::setup() {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Scafacos::compute(int eflag, int vflag)
|
||||
{
|
||||
double **x = atom->x;
|
||||
double *q = atom->q;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// if simluation box has changed, call fcs_tune()
|
||||
|
||||
if (box_has_changed()) {
|
||||
printf("AAA\n");
|
||||
setup_handle();
|
||||
result = fcs_tune(fcs,nlocal,&x[0][0],q);
|
||||
check_result(result);
|
||||
}
|
||||
|
||||
// grow epot & efield if necessary
|
||||
|
||||
if (nlocal > maxatom) {
|
||||
memory->destroy(epot);
|
||||
memory->destroy(efield);
|
||||
maxatom = atom->nmax;
|
||||
memory->create(epot,maxatom,"scafacos:epot");
|
||||
memory->create(efield,maxatom,3,"scafacos:efield");
|
||||
|
||||
}
|
||||
|
||||
// initialize epot & efield
|
||||
// NOTE: is this necessary?
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
epot[i] = 0.0;
|
||||
efield[i][0] = efield[i][1] = efield[i][2] = 0.0;
|
||||
}
|
||||
|
||||
// ScaFaCoS calculation of full Coulombics
|
||||
|
||||
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
|
||||
check_result(result);
|
||||
|
||||
// apply Efield to each particle
|
||||
// accumulate total energy
|
||||
|
||||
double **f = atom->f;
|
||||
|
||||
double qone;
|
||||
double myeng = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
qone = q[i];
|
||||
f[i][0] += qone * efield[i][0];
|
||||
f[i][1] += qone * efield[i][1];
|
||||
f[i][2] += qone * efield[i][2];
|
||||
myeng += 0.5 * qone * epot[i];
|
||||
}
|
||||
|
||||
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Scafacos::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
bytes += maxatom * sizeof(double);
|
||||
bytes += 3*maxatom * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup of ScaFaCoS handle with common parameters
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Scafacos::setup_handle()
|
||||
{
|
||||
// store simulation box params
|
||||
// NOTE: this assumes orthogonal box
|
||||
// NOTE: total particles may not be a 4-byte int
|
||||
// NOTE: what does SCFCS mean by offset?
|
||||
// it's an integer flag in LAMMPS
|
||||
|
||||
old_periodicity[0] = domain->xperiodic;
|
||||
old_periodicity[1] = domain->yperiodic;
|
||||
old_periodicity[2] = domain->zperiodic;
|
||||
|
||||
old_offset[0] = domain->boundary[0][0];
|
||||
old_offset[1] = domain->boundary[1][0];
|
||||
old_offset[2] = domain->boundary[2][0];
|
||||
|
||||
old_box_x[0] = domain->prd[0];
|
||||
old_box_x[1] = old_box_x[2] = 0.0;
|
||||
old_box_y[1] = domain->prd[1];
|
||||
old_box_y[0] = old_box_y[2] = 0.0;
|
||||
old_box_z[2] = domain->prd[2];
|
||||
old_box_z[1] = old_box_z[0] = 0.0;
|
||||
|
||||
old_natoms = atom->natoms;
|
||||
|
||||
// set all required ScaFaCoS params
|
||||
|
||||
result = fcs_set_box_a(fcs,old_box_x);
|
||||
check_result(result);
|
||||
|
||||
result = fcs_set_box_b(fcs,old_box_y);
|
||||
check_result(result);
|
||||
|
||||
result = fcs_set_box_c(fcs,old_box_z);
|
||||
check_result(result);
|
||||
|
||||
result = fcs_set_box_origin(fcs,old_offset);
|
||||
check_result(result);
|
||||
|
||||
result = fcs_set_periodicity(fcs,old_periodicity);
|
||||
check_result(result);
|
||||
|
||||
result = fcs_set_total_particles(fcs,old_natoms);
|
||||
check_result(result);
|
||||
|
||||
// NOTE: for now disable short-range calculations within LAMMPS
|
||||
|
||||
int near_field_flag = 0;
|
||||
result = fcs_set_near_field_flag(fcs,near_field_flag);
|
||||
check_result(result);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if box parameters changed, requiring a new call to fcs_tune
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bool Scafacos::box_has_changed()
|
||||
{
|
||||
int *periodicity = domain->periodicity;
|
||||
double *prd = domain->prd;
|
||||
|
||||
bool changed =
|
||||
(periodicity[0] != old_periodicity[0]) ||
|
||||
(periodicity[1] != old_periodicity[1]) ||
|
||||
(periodicity[2] != old_periodicity[2]) ||
|
||||
(domain->boundary[0][0] != old_offset[0]) ||
|
||||
(domain->boundary[1][0] != old_offset[1]) ||
|
||||
(domain->boundary[2][0] != old_offset[2]) ||
|
||||
(prd[0] != old_box_x[0]) ||
|
||||
(prd[1] != old_box_y[1]) ||
|
||||
(prd[2] != old_box_z[2]) ||
|
||||
(atom->natoms != old_natoms);
|
||||
|
||||
return changed;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check ScaFaCoS result for error condition
|
||||
NOTE: will all procs have same error?
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Scafacos::check_result(FCSResult result)
|
||||
{
|
||||
if (!result) return;
|
||||
|
||||
std::stringstream ss;
|
||||
ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
|
||||
<< fcs_result_get_message(result) << "\n";
|
||||
fcs_result_destroy(result);
|
||||
std::string err_msg = ss.str();
|
||||
const char *str = err_msg.c_str();
|
||||
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef KSPACE_CLASS
|
||||
|
||||
KSpaceStyle(scafacos,Scafacos)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_SCAFACOS_H
|
||||
#define LMP_SCAFACOS_H
|
||||
|
||||
#include "kspace.h"
|
||||
#include "fcs.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class Scafacos : public KSpace {
|
||||
public:
|
||||
Scafacos(class LAMMPS *, int, char **);
|
||||
~Scafacos();
|
||||
void init();
|
||||
void setup();
|
||||
void compute(int, int);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int me;
|
||||
|
||||
char *method;
|
||||
double tolerance;
|
||||
double *epot,**efield;
|
||||
int tolerance_type;
|
||||
int initialized,maxatom;
|
||||
|
||||
FCS fcs; // ScaFaCoS handle
|
||||
FCSResult result; // result for each ScaFaCoS call
|
||||
|
||||
// simulation state: box, natoms
|
||||
// so ScaFaCoS can detect if changes, e.g. for NPT
|
||||
|
||||
fcs_float old_box_x[3],old_box_y[3],old_box_z[3];
|
||||
fcs_float old_offset[3];
|
||||
fcs_int old_periodicity[3];
|
||||
fcs_int old_natoms;
|
||||
|
||||
void check_result(FCSResult);
|
||||
void setup_handle();
|
||||
bool box_has_changed();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue