diff --git a/src/Make.py b/src/Make.py
deleted file mode 100755
index c704cb7037..0000000000
--- a/src/Make.py
+++ /dev/null
@@ -1,880 +0,0 @@
-#!/usr/bin/env python
-# if necessary, edit preceding line to point to your Python
-# or launch as "python Make.py ..."
-
-# Purpose: manage LAMMPS packages, external libraries, and builds
-#          create a version of LAMMPS specific to an input script(s)
-# Syntax: Make.py switch args ...
-# Help: type Make.py or Make.py -h
-
-# -----------------------------------------------------------------------
-# 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.
-# -----------------------------------------------------------------------
-
-# hi-level tasks that can be performed:
-
-# install/uninstall packages and build the associated external libs
-#   use -p and -u and -e
-# install packages needed for input script(s)
-#   use -i and -p
-# create new dir with only the source code needed for input script(s)
-#   use -i and -n
-# build LAMMPS, either in src or new dir
-#   use -b
-
-# data structures:
-
-# packstd list = ["COLLOID", "GPU", ...]
-# packuser list = ["USER-SPH", "USER-EWALDN", ...]
-# cfiles,hfiles dicts of LAMMPS *.cpp,*.h files =
-#   {"fix_nve.cpp": "", "angle_diplole.cpp": "USER-MISC", ...}
-# cdep,hdep dicts of files with list of LAMMPS *.h files they include = 
-#   {"fix_nve.cpp": ['fix_nve.h', 'atom.h', 'force.h', ...'], ...}
-# creq,hreq lists of src files needed to build LAMMPS for input scripts =
-#   ["main.cpp", "atom.cpp", ...]
-
-# ISSUES:
-
-# see KLUDGE comments
-# add more general input script parsing, see NOTE comments
-#   including another file
-#   variable substitution could be used to create new command (hard)
-#   single/double quotes could affect args and hide nested commands
-#   hybrid styles can have required sub-styles
-#   if-then-else and run every could nest other commands as args
-# special case: linalg sometimes needed with ATC external lib
-#               could scan atc/Makefile.lammps for it
-# can long makes print incrementally to screen as they progress?
-# add a verbose output option?
-
-# -----------------------------------------------------------------------
-# -----------------------------------------------------------------------
-
-import sys,glob,re,os,commands
-
-# -----------------------------------------------------------------------
-# variables
-
-# support files in lammps/src neeeded for a build
-
-support = ["Makefile","Make.sh","Makefile.package.empty",
-           "Makefile.package.settings.empty"]
-
-# packages that have external libs with their external lib dir
-
-extlibs = {"USER-ATC": "atc", "USER-AWPMD": "awpmd", "USER-COLVARS": "colvars",
-           "USER-CUDA": "cuda","GPU": "gpu","MEAM": "meam", "POEMS": "poems",
-           "USER-QMMM": "qmmm", "REAX": "reax"}
-
-# help messages
-
-syntax_message = """
-Make.py switch args ...
-Switches: -i file1 file2 ...
-          -p package1 package2 ...
-          -u package1 package2 ...
-          -e package1 arg1 arg2 package2 ...
-          -o dir
-          -b machine
-          -s suffix1 suffix2 ...
-          -l dir
-          -j N
-          -h switch1 switch2 ...
-Help: Make.py or Make.py -h
-"""
-
-ihelp = """
--i file1 file2 ...
-scan input scripts, make list of needed files and packages
-"""
-
-phelp = """
--p package1 package2 ...
-specify zero or more packages
-can use "all" or "standard" or "user"
-install packages required by -i input scripts
-also install listed packages
-"""
-
-uhelp = """
--u package1 package2 ...
-specify zero or more packages
-can specify "all" or "standard" or "user", or package w/out user prefix
-uninstall packages not required by -i input scripts
-also uninstall listed packages
-"""
-
-ehelp = """
--e package1 arg1 arg2 package2 ...
-build external libs for zero or more packages
-can specify package w/out user prefix
-each package can have 1 or 2 optional args
-  arg1 = suffix for lib Makefile
-  arg2 = suffix for lib Makefile.lammps
-example packages with external libs: "gpu", "meam", "user-cuda"
-build external libs for packages required by -i input scripts
-also build external libs for installed packages if none listed
-also build external libs for listed packages
-if arg1 specified, use Makefile.arg1 to build lib, else use Makefile
-if arg2 specified, copy Makefile.lammps.arg2 to Makefile.lammps,
-  else copy Makefile.lammps.arg1 to Makefile.lammps, else do nothing
-"""
-
-ohelp = """
--o newdir
-create newdir with exactly the needed src files for -i input scripts
-newdir will be at same level as src so LAMMPS build will work
-requires use of -i, cannot use with -p or -u
-newdir will include STUBS and MAKE, but no package dirs
-"""
-
-bhelp = """
--b machine
-build LAMMPS in src or newdir using Makefile.machine
-assumes external package libs are already built
-if no -o, build in src
-if -o, build in newdir, including STUBS build if needed
-"""
-
-shelp = """
--s suffix1 suffix2 ...
-specify optimization suffixes to add to style names in -i input scripts
-requires use of -i
-same suffixes as LAMMPS -s command-line switch allows
-example suffixes = "opt", "gpu", "cuda", "omp"
-"""
-
-lhelp = """
--l dir
-specify LAMMPS home dir
-required if not running Make.py from within lammps/src
-"""
-
-jhelp = """
--j N
-perform LAMMPS and external lib builds in parallel
-adds "-j N" switch to "make" commands
-N = 0 performs serial make
-default N = 16
-"""
-
-hhelp = """
-Make.py lists all switches
-Make.py -h -i -b ... gives help on each switch
-Make.py -h gives this message
-"""
-
-# -----------------------------------------------------------------------
-# functions
-
-# print syntax message
-
-def syntax():
-  print syntax_message
-  sys.exit()
-
-# help messages
-
-def helptxt(switches):
-  if not switches: switches = ["-h"]
-  for sw in switches:
-    if sw == "-i": print ihelp
-    elif sw == "-p": print phelp
-    elif sw == "-u": print uhelp
-    elif sw == "-e": print ehelp
-    elif sw == "-o": print ohelp
-    elif sw == "-b": print bhelp
-    elif sw == "-s": print shelp
-    elif sw == "-l": print lhelp
-    elif sw == "-j": print jhelp
-    elif sw == "-h": print hhelp
-    else: error("Invalid help switch")
-
-# print error message
-
-def error(str):
-  print "ERROR:",str
-  sys.exit()
-  
-# convert *.cpp file to *.h file
-
-def c2h(file):
-  return file[:-4] + ".h"
-  
-# convert *.h file to *.cpp file
-
-def h2c(file):
-  return file[:-2] + ".cpp"
-  
-# append file to list
-# but only if file is not already in list
-# but only if file is in cfiles or hfiles
-
-def addfile(file,list):
-  if file in list: return
-  if file not in cfiles and file not in hfiles: return
-  list.append(file)
-
-# grab list of LAMMPS package dirs from src/Makefile
-  
-def lammps_packages():
-  txt = open(srcdir + "/Makefile",'r').read()
-  pattern = "PACKAGE = (.*?)\n\n"
-  match = re.search(pattern,txt,re.DOTALL)
-  packstd = match.group(1).replace("\\","").upper().split()
-  pattern = "PACKUSER = (.*?)\n\n"
-  match = re.search(pattern,txt,re.DOTALL)
-  packuser = match.group(1).replace("\\","").upper().split()
-  return packstd,packuser
-
-# uninstall package in LAMMPS src dir
-# package can be upper-case or lower-case
-
-def uninstall_package(package):
-  package = package.lower()
-  cmd = "cd %s; make no-%s" % (srcdir,package)
-  commands.getoutput(cmd)
-  print "  uninstalled",package
-  
-# install package in LAMMPS src dir
-# package can be upper-case or lower-case
-
-def install_package(package):
-  package = package.lower()
-  cmd = "cd %s; make yes-%s" % (srcdir,package)
-  commands.getoutput(cmd)
-  print "  installed",package
-
-# re-parse list of packages input via -e switch
-# one or two flags may be appended to a package
-# convert into dict with value = list of flags
-
-def reparse_packages(packages):
-  dict = {}
-  last = ""
-  for package in packages:
-    upper = package.upper()
-    flag = 0
-    if upper in packstd: flag = 1
-    elif upper in packuser: flag = 1
-    elif "USER-" + upper in packuser: flag = 1
-    if flag:
-      dict[package] = []
-      last = package
-    else:
-      if not last: error("Invalid package in -e list")
-      buildflags = dict[last]
-      if len(buildflags) == 2:
-        error("Too many machine flags appended to package %s" % last)
-      buildflags.append(package)
-  return dict
-
-# detect which packages are installed via "make package-status" command
-# return as list
-
-def detect_installed_packages():
-  cmd = "cd %s; make package-status" % srcdir
-  output = commands.getoutput(cmd)
-  pattern = "Installed\s*(.*): package (.*)"
-  status = re.findall(pattern,output)
-  installed = []
-  for entry in status:
-    if entry[0] == "YES": installed.append(entry[1])
-  return installed
-  
-# create dict of all LAMMPS *.cpp and *.h files with no duplicates
-# key = file
-# value = package dir if file in a package dir
-# value = empty if file is only in lammps/src
-# discard style_*.h files
-
-def lammps_files():
-  files = []
-  for dir in packstd:
-    files += glob.glob(dir + "/*.cpp")
-    files += glob.glob(dir + "/*.h")
-  for dir in packuser:
-    files += glob.glob(dir + "/*.cpp")
-    files += glob.glob(dir + "/*.h")
-  files += glob.glob("*.cpp")
-  files += glob.glob("*.h")
-
-  cfiles = {}
-  hfiles = {}
-  for file in files:
-    dir = os.path.dirname(file)
-    file = os.path.basename(file)
-    if file.find("style_") == 0: continue
-    if file[-2:] == ".h":
-      if file not in hfiles: hfiles[file] = dir
-    else:
-      if file not in cfiles: cfiles[file] = dir
-      
-  return cfiles,hfiles
-
-# parse each cfile,hfile to find list of LAMMPS *.h files it includes
-# create cdep,hdep = dict with key = filename, value = list of *.h files
-# KLUDGE for accelerator_cuda.h to ignore the *.h files it includes
-#        when "cuda" is not explicitly listed as a suffix,
-#        this is b/c it has an ifdef that includes several *cuda*.h files
-
-def dependencies():
-  pattern = re.compile('^#include "(.+?)"',re.MULTILINE)
-
-  cdep = {}
-  for file in cfiles:
-    if cfiles[file]: file = cfiles[file] + "/" + file
-    txt = open(file,'r').read()
-    possible = re.findall(pattern,txt)
-    depends = []
-    for dfile in possible:
-      if dfile in hfiles: depends.append(dfile)
-    cdep[os.path.basename(file)] = depends
-
-  hdep = {}
-  for file in hfiles:
-    if hfiles[file]: file = hfiles[file] + "/" + file
-    txt = open(file,'r').read()
-    possible = re.findall(pattern,txt)
-    depends = []
-    for dfile in possible:
-      if dfile in hfiles: depends.append(dfile)
-    if file == "accelerator_cuda.h" and "cuda" not in suffixes: depends = []
-    hdep[os.path.basename(file)] = depends
-
-  return cdep,hdep
-
-# add style files referenced in input script to lookup list
-# parse input script lines to look for them
-# add suffix for certain styles
-
-def need_from_input_script(file,lookup):
-  lines = open(file,'r').readlines()
-
-  # skip comment and blank lines
-  # NOTE: need to treat concatenated lines
-  # NOTE: need to handle quoted args when split into words
-  # NOTE: need to treat if and run every and print, which nest commands
-
-  cmds = {}
-  for line in lines:
-    if line.find("#") >= 0: line = line[:line.find("#")]
-    line = line.strip()
-    if len(line) == 0: continue
-    words = line.split()
-    cmds[words[0]] = words[1:]
-
-  # for commands with styles, generate file associated with style name
-  # suffixes induce multiple file variants
-  # final else handles command styles if "CommandStyle" found in *.h file
-    
-  for cmd in cmds:
-    args = cmds[cmd]
-    files = []
-    if cmd == "atom_style":
-      files.append("atom_vec_" + args[0])
-      for suffix in suffixes: files.append("atom_vec_" + args[0] + "/" + suffix)
-    elif cmd == "pair_style":
-      files.append("pair_" + args[0])
-      for suffix in suffixes: files.append("pair_" + args[0] + "/" + suffix)
-    elif cmd == "bond_style":
-      files.append("bond_" + args[0])
-      for suffix in suffixes: files.append("bond_" + args[0] + "/" + suffix)
-    elif cmd == "angle_style":
-      files.append("angle_" + args[0])
-      for suffix in suffixes: files.append("angle_" + args[0] + "/" + suffix)
-    elif cmd == "dihedral_style":
-      files.append("dihedral_" + args[0])
-      for suffix in suffixes: files.append("dihedral_" + args[0] + "/" + suffix)
-    elif cmd == "improper_style":
-      files.append("improper_" + args[0])
-      for suffix in suffixes: files.append("improper_" + args[0] + "/" + suffix)
-    elif cmd == "kspace_style":
-      files.append(args[0])
-      for suffix in suffixes: files.append(args[0] + "/" + suffix)
-    elif cmd == "run_style":
-      files.append(args[0])
-      for suffix in suffixes: files.append(args[0] + "/" + suffix)
-    elif cmd == "min_style":
-      files.append("min_" + args[0])
-    elif cmd == "compute":
-      files.append("compute_" + args[2])
-      for suffix in suffixes: files.append("compute_" + args[2] + "/" + suffix)
-    elif cmd == "dump":
-      files.append("dump_" + args[2])
-    elif cmd == "fix":
-      files.append("fix_" + args[2])
-      for suffix in suffixes: files.append("fix_" + args[2] + "/" + suffix)
-    elif cmd == "region":
-      files.append("region_" + args[1])
-    else:
-      tmpfile = cmd + ".cpp"
-      if tmpfile not in cfiles: continue
-      if cfiles[tmpfile]: tmpfile = cfiles[tmpfile] + "/" + tmpfile
-      txt = open(c2h(tmpfile)).read()
-      if not "CommandStyle" in txt: continue
-      files.append(cmd)
-
-    for file in files:
-      file = file.replace("/","_") + ".cpp"
-      addfile(file,lookup)
-
-# add additional CPP files required to build LAMMPS to lookup list
-# always add main.cpp
-# always add atom_vec_atomic,
-#   since Atom class creates it directly
-# always add compute_temp, compute_pe, compute_pressure,
-#   since Output class creates these computes directly
-# always add verlet and min_cg,
-#   since Update class creates them directly
-# always add src/neigh_*.cpp since are part of Neighbor class,
-#   but only neighbor.cpp is inferred by neighbor.h
-# KLUDGE:
-#   likewise add USER-OMP/neigh_*.cpp if any USER-OMP files are in lookup
-#   likewise add USER-CUDA/neigh_*.cpp if any USER-CUDA files are in lookup
-      
-def need_additional(lookup):
-  addfile("main.cpp",lookup)
-  addfile("atom_vec_atomic.cpp",lookup)
-  addfile("compute_temp.cpp",lookup)
-  addfile("compute_pe.cpp",lookup)
-  addfile("compute_pressure.cpp",lookup)
-  addfile("verlet.cpp",lookup)
-  addfile("min_cg.cpp",lookup)
-
-  user_cuda = user_omp = 0
-  for file in lookup:
-    if file[-2:] == ".h":
-      if hfiles[file] == "USER-CUDA": user_cuda = 1
-      if hfiles[file] == "USER-OMP": user_omp = 1
-    else:
-      if cfiles[file] == "USER-CUDA": user_cuda = 1
-      if cfiles[file] == "USER-OMP": user_omp = 1
-    
-  for file in cfiles:
-    if file.find("neigh_") == 0:
-      if cfiles[file] == "": addfile(file,lookup)
-      if cfiles[file] == "USER-CUDA" and user_cuda: addfile(file,lookup)
-      if cfiles[file] == "USER-OMP" and user_omp: addfile(file,lookup)
-
-# creq,hreq = list of all CPP and H files needed to build LAMMPS
-# inferred from lookup list and each file's dependencies in cdep,hdep
-# when an H file is added, also add corresponding CPP file to lookup
-# addfile insures no duplicates in creq,hreq
-
-def resolve_dependencies(lookup):
-  creq = []
-  hreq = []
-
-  i = 0
-  while i < len(lookup):
-    file = lookup[i]
-    if file[-2:] == ".h":
-      hreq.append(file)
-      dfiles = hdep[file]
-      addfile(h2c(file),lookup)
-    else:
-      creq.append(file)
-      dfiles = cdep[file]
-    for dfile in dfiles: addfile(dfile,lookup)
-    i += 1
-    
-  return creq,hreq
-
-# -----------------------------------------------------------------------
-# main program
-
-# defaults
-
-infiles = []
-packflag = 0
-packages = []
-unpackflag = 0
-unpackages = []
-extflag = 0
-extpackages = []
-newdir = ""
-build = ""
-suffixes = []
-lammpsdir = ""
-jmake = 16
-helpflag = 0
-help = []
-
-# parse command-line args
-
-args = sys.argv
-narg = len(args)
-
-if narg == 1: syntax()
-
-iarg = 1
-while iarg < narg:
-  if args[iarg] == "-i":
-    if iarg+2 > narg: syntax()
-    iarg += 1
-    while iarg < narg and args[iarg][0] != '-':
-      infiles.append(args[iarg])
-      iarg += 1
-  elif args[iarg] == "-p":
-    packflag = 1
-    iarg += 1
-    while iarg < narg and args[iarg][0] != '-':
-      packages.append(args[iarg])
-      iarg += 1
-  elif args[iarg] == "-u":
-    unpackflag = 1
-    iarg += 1
-    while iarg < narg and args[iarg][0] != '-':
-      unpackages.append(args[iarg])
-      iarg += 1
-  elif args[iarg] == "-e":
-    extflag = 1
-    iarg += 1
-    while iarg < narg and args[iarg][0] != '-':
-      extpackages.append(args[iarg])
-      iarg += 1
-  elif args[iarg] == "-o":
-    if iarg+2 > narg: syntax()
-    newdir = args[iarg+1]
-    iarg += 2
-  elif args[iarg] == "-b":
-    if iarg+2 > narg: syntax()
-    build = args[iarg+1]
-    iarg += 2
-  elif args[iarg] == "-s":
-    if iarg+2 > narg: syntax()
-    iarg += 1
-    while iarg < narg and args[iarg][0] != '-':
-      suffixes.append(args[iarg])
-      iarg += 1
-  elif args[iarg] == "-l":
-    if iarg+2 > narg: syntax()
-    lammpsdir = args[iarg+1]
-    iarg += 2
-  elif args[iarg] == "-j":
-    if iarg+2 > narg: syntax()
-    jmake = int(args[iarg+1])
-    iarg += 1
-  elif args[iarg] == "-h":
-    helpflag = 1
-    iarg += 1
-    while iarg < narg and args[iarg][0] == '-':
-      help.append(args[iarg])
-      iarg += 1
-  else: syntax()
-
-# help
-
-if helpflag: helptxt(help)
-  
-# error check
-
-if newdir:
-  if not infiles: error("Cannot use -o without -i")
-  if packflag: error("Cannot use -o with -p")
-  if unpackages: error("Cannot use -o with -u")
-
-if suffixes:
-  if not infiles: error("Cannot use -s without -i")
-
-# setup strings
-# srcdir = LAMMPS src dir
-# check that srcdir is valid via 2 "empty" files and version.h
-# libdir = LAMMPS lib dir
-# newdir = new src dir
-# makestr = -j N for parallel make
-  
-if lammpsdir: srcdir = lammpsdir + "/src"
-else: srcdir = "."
-
-if not os.path.isfile(srcdir + "/Makefile.package.empty") \
-      or not os.path.isfile(srcdir + "/Makefile.package.settings.empty") \
-      or not os.path.isfile(srcdir + "/version.h"):
-  error("Not running in LAMMPS src dir, use -l switch")
-
-if srcdir == ".": libdir = "../lib"
-else: libdir = srcdir[:-3] + "lib"
-
-if newdir:
-  if srcdir == ".": newdir = "../" + newdir
-  else: newdir = srcdir[:-3] + newdir
-
-if jmake == 0: makestr = ""
-else: makestr = "-j %d" % jmake
-  
-# packstd,packuser = list of package dirs in lammps/src
-
-packstd,packuser = lammps_packages()
-
-# -i switch
-# cfiles,hfiles = all LAMMPS src files
-# cdep,hdep = src files with list of *.h files each depends on
-# lookup = needed *.cpp files = default + input script styles
-# creq,hreq = files needed to build LAMMPS = lookup + dependencies
-# packneed = needed packages
-
-if infiles:
-  print "Scanning input scripts ..."
-  cfiles,hfiles = lammps_files()
-  cdep,hdep = dependencies()
-  lookup = []
-  for file in infiles: need_from_input_script(file,lookup)
-  need_additional(lookup)
-  creq,hreq = resolve_dependencies(lookup)
-  
-  packneed = []
-  for file in creq:
-    if cfiles[file] and cfiles[file] not in packneed:
-      packneed.append(cfiles[file])
-  for file in hreq:
-    if hfiles[file] and hfiles[file] not in packneed:
-      packneed.append(hfiles[file])
-
-  print "  scripts require %d LAMMPS *.cpp files" % len(creq)
-  print "  scripts require %d LAMMPS *.h files" % len(hreq)
-  print "  scripts require %d packages:" % len(packneed),
-  print packneed
-
-# -u switch
-# if -i, add unneeded packages to list
-# add explicitly named packages to list
-# uninstall packages in list only if installed
-
-if unpackflag:
-  print "Uninstalling packages ..."
-  
-  list = []
-  if infiles:
-    for package in packstd:
-      if package not in packneed: list.append(package)
-    for package in packuser:
-      if package not in packneed: list.append(package)
-  for entry in unpackages:
-    entry = entry.upper()
-    if entry == "ALL":
-      for package in packstd:
-        if package not in list: list.append(package)
-      for package in packuser:
-        if package not in list: list.append(package)
-    elif entry == "STANDARD":
-      for package in packstd:
-        if package not in list: list.append(package)
-    elif entry == "USER":
-      for package in packuser:
-        if package not in list: list.append(package)
-    elif entry in packstd:
-      if entry not in list: list.append(entry)
-    elif entry in packuser:
-      if entry not in list: list.append(entry)
-    elif "USER-" + entry in packuser:
-      if "USER-" + entry not in list: list.append("USER-" + entry)
-    else: error("Invalid package %s to uninstall" % entry.lower())
-
-  installed_packages = detect_installed_packages()
-  for package in list:
-    if package in installed_packages: uninstall_package(package)
-    
-# -p switch
-# if -i, add needed packages to list
-# add explicitly named packages to list
-# install packages in list only if uninstalled
-
-if packflag:
-  print "Installing packages ..."
-  
-  list = []
-  if infiles:
-    for package in packneed: list.append(package)
-  for entry in packages:
-    entry = entry.upper()
-    if entry == "ALL":
-      for package in packstd:
-        if package not in list: list.append(package)
-      for package in packuser:
-        if package not in list: list.append(package)
-    elif entry == "STANDARD":
-      for package in packstd:
-        if package not in list: list.append(package)
-    elif entry == "USER":
-      for package in packuser:
-        if package not in list: list.append(package)
-    elif entry in packstd:
-      if entry not in list: list.append(entry)
-    elif entry in packuser:
-      if entry not in list: list.append(entry)
-    elif "USER-" + entry in packuser:
-      if "USER-" + entry not in list: list.append("USER-" + entry)
-    else: error("Invalid package %s to install" % entry.lower())
-
-  installed_packages = detect_installed_packages()
-  for package in list:
-    if package not in installed_packages: install_package(package)
-
-# -e switch
-# add explicitly named libs to list first, so can include arg1/arg2
-# if -i, add needed libs to list
-# if none named, add libs for installed packages to list
-# use Makefile.arg1 and Makefile.lammps.arg1/arg2 if specified
-# force rebuild by doing clean first
-    
-if extflag:
-  print "Building external libraries ..."
-
-  list = {}
-  packages_with_flags = reparse_packages(extpackages)
-  for package in packages_with_flags:
-    upper = package.upper()
-    if upper in extlibs and upper not in list:
-      list[upper] = packages_with_flags[package]
-    upper = "USER-" + upper
-    if upper in extlibs and upper not in list:
-      list[upper] = packages_with_flags[package]
-
-  if infiles:
-    for package in packneed:
-      if package in extlibs and package not in list: list[package] = []
-  if not extpackages:
-    installed_packages = detect_installed_packages()
-    for package in installed_packages:
-      if package in extlibs and package not in list: list[package] = []
-    
-  for package in list:
-    lib = extlibs[package]
-    print "  lib/%s/lib%s.a for package %s ..." % (lib,lib,package)
-    args = list[package]
-
-    # makefile = Makefile by default unless arg1 specified
-    
-    makefile = "Makefile"
-    if args: makefile = "Makefile.%s" % args[0]
-    if not os.path.isfile("%s/%s/%s" % (libdir,lib,makefile)):
-      error("%s for external lib %s does not exist" % (makefile,lib))
-
-    # no makefile_lammps by default unless arg2 or arg1 specified
-      
-    makefile_lammps = ""
-    if args and len(args) == 2:
-      makefile_lammps = "Makefile.lammps.%s" % args[1]
-      if not os.path.isfile("%s/%s/%s" % (libdir,lib,makefile_lammps)):
-        error("%s for external lib %s does not exist" % (makefile,lib))
-    elif args:
-      makefile_lammps = "Makefile.lammps.%s" % args[0]
-
-    # target lib file
-    # KLUDGE for cuda, since it is liblammpscuda.a instead of libcuda.a
-      
-    libfile = "%s/%s/lib%s.a" % (libdir,lib,lib)
-    if lib == "cuda": libfile = "%s/%s/liblammpscuda.a" % (libdir,lib)
-    
-    # remove lib file
-
-    if os.path.exists(libfile): os.remove(libfile)
-    
-    # make clean
-
-    print "    cleaning ..."
-    cmd = "cd %s/%s; make -f %s clean" % (libdir,lib,makefile)
-    output = commands.getoutput(cmd)
-
-    # build the external lib and check if successful
-      
-    print "    building ..."
-    cmd = "cd %s/%s; make %s -f %s" % (libdir,lib,makestr,makefile)
-    output = commands.getoutput(cmd)
-    if os.path.exists(libfile):
-      print "  successfully built lib/%s/lib%s.a" % (lib,lib)
-    else:
-      print output
-      error("Build of lib/%s/lib%s.a was unsuccessful" % (lib,lib))
-
-    # if it exists, copy makefile_lammps to Makefile.lammps
-
-    if makefile_lammps:
-      if os.path.isfile("%s/%s/%s" % (libdir,lib,makefile_lammps)):
-        cmd = "cd %s/%s; cp %s Makefile.lammps" % (libdir,lib,makefile_lammps) 
-        commands.getoutput(cmd)
-
-# -n switch
-# create newdir with exactly the needed src files for scripts
-# newdir has support files and STUBS and MAKE, but no package dirs
-# insure Makefile.package and Makefile.package.settings are correct by
-#   installing all needed packages in newdir, then delete package dirs
-
-if newdir:
-  print "Creating %s ..." % newdir
-  if os.path.exists(newdir): error("Directory %s already exists" % newdir)
-  os.mkdir(newdir)
-  os.mkdir(newdir + "/MAKE")
-  os.mkdir(newdir + "/STUBS")
-    
-  for file in support:
-    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
-
-  files = glob.glob("%s/MAKE/Makefile.*" % srcdir)
-  fstr = " ".join(files)
-  commands.getoutput("cp %s %s/MAKE" % (fstr,newdir))
-
-  commands.getoutput("cp %s/STUBS/Makefile %s/STUBS" % (srcdir,newdir))
-  commands.getoutput("cp %s/STUBS/mpi.c %s/STUBS" % (srcdir,newdir))
-  commands.getoutput("cp %s/STUBS/mpi.h %s/STUBS" % (srcdir,newdir))
-
-  for package in packneed:
-    os.mkdir("%s/%s" % (newdir,package))
-    commands.getoutput("cp %s/%s/* %s/%s" % (srcdir,package,newdir,package))
-    commands.getoutput("cd %s; make yes-%s" % (newdir,package.lower()))
-    commands.getoutput("rm -r %s/%s" % (newdir,package))
-
-  commands.getoutput("rm -r %s/*.cpp" % (newdir))
-  commands.getoutput("rm -r %s/*.h" % (newdir))
-    
-  for file in creq:
-    if cfiles[file]: file = cfiles[file] + "/" + file
-    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
-  for file in hreq:
-    if hfiles[file]: file = hfiles[file] + "/" + file
-    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
-
-# -b switch
-# build LAMMPS in src or newdir
-# assumes external package libs are already built
-# build STUBS lib if needed and not already built
-    
-if build:
-  print "Building LAMMPS for %s ..." % build
-  if newdir: builddir = newdir
-  else: builddir = srcdir
-
-  makefile = "%s/MAKE/Makefile.%s" % (builddir,build)
-  if not os.path.exists(makefile):
-    error("%s does not exist" % makefile)
-
-  txt = open(makefile,"r").read()
-  if "../STUBS" in txt:
-    if not os.path.exists("%s/STUBS/libmpi.a" % builddir):
-      cmd = "cd %s/STUBS; make" % builddir
-      output = commands.getoutput(cmd)
-      if os.path.exists("%s/STUBS/libmpi.a" % builddir):
-        print "Successfully built STUBS/libmpi.a"
-      else:
-        print output
-        error("Build of STUBS/libmpi.a was unsuccessful")
-    
-  if os.path.exists("%s/lmp_%s" % (builddir,build)):
-    os.remove("%s/lmp_%s" % (builddir,build))
-  cmd = "cd %s; make %s %s" % (builddir,makestr,build)
-  output = commands.getoutput(cmd)
-  if os.path.exists("%s/lmp_%s" % (builddir,build)):
-    print "Successfully built %s/lmp_%s" % (builddir,build)
-  else:
-    print output
-    error("Build of %s/lmp_%s was unsuccessful" % (builddir,build))