better Install.py script for KIM from Ryan Elliott

doc/src/Section_example.txt

@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field

doc/src/Section_packages.txt

@@ -492,14 +492,38 @@ Minnesota).
 
 [Install or un-install:]
 
-Using this package requires the KIM library and its models
+Before building LAMMPS with this package, you must first download and
-(interatomic potentials) to be downloaded and installed on your
+build the KIM library and include the KIM models that you want to
-system.  The library can be downloaded and built in lib/kim or
+use. You can do this manually if you prefer; follow the instructions
-elsewhere on your system.  Details of the download, build, and install
+in lib/kim/README.  You can also do it in one step from the lammps/src
-process for KIM are given in the lib/kim/README file.
+dir, using a command like these, which simply invoke the
+lib/kim/Install.py script with the specified args.
 
-Once that process is complete, you can then install/un-install the
+make lib-kim                    # print help message
-package and build LAMMPS in the usual manner:
+make lib-kim args="-b . none"   # install KIM API lib with only example models
+make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b . OpenKIM"   # install KIM API lib with all models
+make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002"   # add one model or model driver :pre
+
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.  Also note that installing the KIM API
+library with all its models, may take around 30 min to build.  Of
+course you only need to do that once.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api
+in the "What is in the KIM API source package?" section
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
 
 make yes-kim
 make machine :pre
@@ -1414,7 +1438,7 @@ lib/linalg.  In the latter case you also need to build the library
 in lib/linalg with a command like these:
 
 make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg args="-m gfortran"   # build with GNU Fortran compiler
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -2469,8 +2493,8 @@ step from the lammps/src dir, using a command like these, which simply
 invoke the lib/smd/Install.py script with the specified args:
 
 make lib-smd                            # print help message
-make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*
+make lib-smd args="-g -l"               # download and build in default lib/smd/eigen-eigen-*
-make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen
+make lib-smd args="-h . eigen -g -l"    # download and build in lib/smd/eigen
 make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre
 
 Note that the final -l switch is to create a symbolic (soft) link

doc/src/neigh_modify.txt

@@ -109,7 +109,8 @@ atoms in the specified group.  This can be useful for models where a
 large portion of the simulation is particles that do not interact with
 other particles or with each other via pairwise interactions.  The
 group specified with this option must also be specified via the
-"atom_modify first"_atom_modify.html command.
+"atom_modify first"_atom_modify.html command.  Note that specifying
+"all" as the group-ID effectively turns off the {include} option.
 
 The {exclude} option turns off pairwise interactions between certain
 pairs of atoms, by not including them in the neighbor list.  These are
@@ -213,5 +214,5 @@ space.
 [Default:]
 
 The option defaults are delay = 10, every = 1, check = yes, once = no,
-cluster = no, include = all, exclude = none, page = 100000, one =
+cluster = no, include = all (same as no include option defined),
-2000, and binsize = 0.0.
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.

examples/README

@@ -58,6 +58,7 @@ These are the sample problems and their output in the various
 sub-directories:
 
 accelerate: use of all the various accelerator packages
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field

lib/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/atc/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/awpmd/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/colvars/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/gpu/Install.py

@@ -8,8 +8,11 @@ import sys,os,re,commands
 # help message
 
 help = """
-Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
+Syntax from src dir: make lib-gpu args="-i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix"
+Syntax from lib dir: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
+
 specify one or more options, order does not matter
+
 copies an existing Makefile.isuffix in lib/gpu to Makefile.auto 
 optionally edits these variables in Makefile.auto:
   CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
@@ -34,6 +37,12 @@ Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m
        also copies EXTRAMAKE file -> Makefile.lammps
          -e can set which Makefile.lammps.esuffix file is copied
   -o = copy final Makefile.auto to Makefile.osuffix
+
+Examples:
+
+make lib-gpu args="-m"      # build GPU lib with default Makefile.linux
+make lib-gpu args="-i xk7 -p single -o xk7.single"      # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-i xk7 -p single -o xk7.single -m"   # ditto, also build GPU lib
 """
 
 # print error message or help

lib/h5md/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/kim/Install.py

@@ -1,25 +1,44 @@
 #!/usr/bin/env python
 
-# install.py tool to setup the kim-api library
+# install.pa tool to setup the kim-api library
 # used to automate the steps described in the README file in this dir
 
 import sys,os,re,urllib,commands
 
 help = """
-Syntax: install.py -v version -c kim-dir -b kim-model-name -a kim-name
+Syntax from src dir: make lib-kim args="-v version -b kim-install-dir kim-name -a kim-name"
+Syntax from lib dir: python Install.py -v version -b kim-install-dir kim-name -a kim-name
+
 specify one or more options, order does not matter
-        -v = version of kim-api to download and work with
+
+  -v = version of KIM API library to use
        default = kim-api-v1.8.2 (current as of June 2017)
-        -c = create Makefile.KIM_DIR within lammps lib/kim to configure lammps
+  -b = download and build KIM API library with KIM models
-             for use with the kim-api library installed at "kim-dir" (absolute
+       kim-dir = where to install/build the KIM API library
-             path).  default = this dir
+         use "." to install in lib/kim
-        -b = build kim-api and kim model where kim-model-name can be a specific
+       kim-name = none to install only the example KIM models
-             openkim.org model name (such as
+       kim-name = KIM model name (see example below) + examples
-             "EAM_Dynamo_Ackland_W__MO_141627196590_002") or the keyword
+       kim-name = OpenKIM to install all models
-             "OpenKIM" to install all compatible models from the openkim.org
+         from the openkim.org site (this can take 30 minutes or more)
-             site.
+  -a = add single KIM model or model driver with kim-name
-        -a = add kim-name openkim.org item (model driver or model) to existing
+       to existing KIM API lib (see example below)
-             kim-api instalation.
+
+Examples:
+
+make lib-kim args="-b . none"   # install KIM API lib with only example models
+make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b . OpenKIM"   # install KIM API lib with all models
+make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002"   # add one model or model driver
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api
+in the "What is in the KIM API source package?" section
 """
 
 def error():
@@ -28,32 +47,28 @@ def error():
 
 # parse args
 
-args = sys.argv
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
 
 thisdir = os.environ['PWD']
-dir = thisdir
 version = "kim-api-v1.8.2"
 
-dirflag = 0
 buildflag = 0
 addflag = 0
 
-iarg = 1
+iarg = 0
 while iarg < len(args):
   if args[iarg] == "-v":
     if iarg+2 > len(args): error()
     version = args[iarg+1]
     iarg += 2
-  elif args[iarg] == "-c":
-    dirflag = 1
-    if iarg+2 > len(args): error()
-    dir = args[iarg+1]
-    iarg += 2
   elif args[iarg] == "-b":
     buildflag = 1
-    if iarg+2 > len(args): error()
+    if iarg+3 > len(args): error()
-    modelname = args[iarg+1]
+    dir = args[iarg+1]
-    iarg += 2
+    modelname = args[iarg+2]
+    iarg += 3
   elif args[iarg] == "-a":
     addflag = 1
     if iarg+2 > len(args): error()
@@ -62,33 +77,59 @@ while iarg < len(args):
   else: error()
 
 thisdir = os.path.abspath(thisdir)
-dir = os.path.abspath(dir)
 url = "https://s3.openkim.org/kim-api/%s.tgz" % version
 
-# download and unpack tarball
+# download KIM tarball, unpack, build KIM
-
+# either in lib/kim or user-requested location
-
-if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir):
-  open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
-  open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
-  print "Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
-else:
-  if dirflag == 1:
-    open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
-    open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
-    print "Updated %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
-
 
 if buildflag == 1:
-  # download kim-api
+
+  # set install directory
+  dir = os.path.abspath(dir) + "/installed-" + version
+
+  # check to see if an installed kim-api already exists
+
+  if os.path.isdir(dir):
+     print "kim-api is already installed at %s" % dir
+     print "Must remove this directory in order to resintall at this location"
+     sys.exit()
+
+  # configure LAMMPS to use kim-api to be installed
+
+  mkfle = open("%s/Makefile.KIM_DIR" % thisdir, 'w')
+  mkfle.write("KIM_INSTALL_DIR=%s\n" % dir)
+  mkfle.write("\n")
+  mkfle.write(".DUMMY: print_dir\n")
+  mkfle.write("\n")
+  mkfle.write("print_dir:\n")
+  mkfle.write("	@printf $(KIM_INSTALL_DIR)\n")
+  mkfle.close()
+  open("%s/Makefile.KIM_Config" % thisdir, 'w'). \
+    write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
+  print "Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
+
+  # download entire kim-api tarball
+  # try first via urllib
+  # if fails (probably due to no SSL support), use wget
+
   print "Downloading kim-api tarball ..."
-  urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,version))
+
+  try: urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,version))
+  except:
+    cmd = "wget %s %s/%s.tgz" % (url,thisdir,version)
+    txt = commands.getstatusoutput(cmd)
+    print txt[1]
+    if not os.path.isfile("%s/%s.tgz" % (thisdir,version)):
+      print "Both urllib.urlretrieve() and wget command failed to download"
+      sys.exit()
+
   print "Unpacking kim-api tarball ..."
   cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version)
   txt = commands.getstatusoutput(cmd)
   if txt[0] != 0: error()
 
   # configure kim-api
+
   print "Configuring kim-api ..."
   cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,dir)
   txt = commands.getstatusoutput(cmd)
@@ -96,12 +137,19 @@ if buildflag == 1:
   if txt[0] != 0: error()
 
   # build kim-api
+
   print "Configuring model : %s" % modelname
-  cmd = "cd %s/%s; make add-%s" % (thisdir,version,modelname)
+  if modelname == "none":
+    cmd = "cd %s/%s; make add-examples" % (thisdir,version)
+  else:
+    if modelname == "OpenKIM":
+      print "configuring all OpenKIM models, this will take a while ..."
+    cmd = "cd %s/%s; make add-examples; make add-%s" % \
+        (thisdir,version,modelname)
   txt = commands.getstatusoutput(cmd)
   print txt[1]
   if txt[0] != 0: error()
-  #
+
   print "Building kim-api ..."
   cmd = "cd %s/%s; make" % (thisdir,version)
   txt = commands.getstatusoutput(cmd)
@@ -109,40 +157,99 @@ if buildflag == 1:
   if txt[0] != 0: error()
 
   # install kim-api
+
   print "Installing kim-api ..."
   cmd = "cd %s/%s; make install" % (thisdir,version)
   txt = commands.getstatusoutput(cmd)
   print txt[1]
   if txt[0] != 0: error()
-  #
+
   cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version)
   txt = commands.getstatusoutput(cmd)
   print txt[1]
   if txt[0] != 0: error()
 
   # remove source files
+
   print "Removing kim-api source and build files ..."
   cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version)
   txt = commands.getstatusoutput(cmd)
   print txt[1]
   if txt[0] != 0: error()
 
+# add a single model (and possibly its driver) to existing KIM installation
+
 if addflag == 1:
-  # download model
+
-  url = "https://openkim.org/download/%s.tgz" % addmodelname
+  # get location of installed kim-api
+
+  if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir):
+    print "kim-api is not installed"
+    error()
+  else:
+    cmd = "cd %s; make -f Makefile.KIM_DIR print_dir" % thisdir
+    dir = commands.getstatusoutput(cmd)[1]
+
+  # download single model
+  # try first via urllib
+  # if fails (probably due to no SSL support), use wget
+
   print "Downloading item tarball ..."
-  urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,addmodelname))
+
+  url = "https://openkim.org/download/%s.tgz" % addmodelname
+
+  try: urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,addmodelname))
+  except:
+    cmd = "wget %s %s/%s.tgz" % (url,thisdir,addmodelname)
+    txt = commands.getstatusoutput(cmd)
+    print txt[1]
+    if not os.path.isfile("%s/%s.tgz" % (thisdir,addmodelname)):
+      print "Both urllib.urlretrieve() and wget command failed to download"
+      sys.exit()
+
   print "Unpacking item tarball ..."
   cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname)
   txt = commands.getstatusoutput(cmd)
   if txt[0] != 0: error()
-  #
+
   print "Building item ..."
   cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname)
   txt = commands.getstatusoutput(cmd)
+  firstRunOutput = txt[1]
+  if txt[0] != 0:
+    # Error: but first, check to see if it needs a driver
+
+    cmd = "cd %s/%s; make kim-item-type" % (thisdir,addmodelname)
+    txt = commands.getstatusoutput(cmd)
+    if txt[1] == "ParameterizedModel":
+
+      # Get and install driver
+
+      cmd = "cd %s/%s; make model-driver-name" % (thisdir,addmodelname)
+      txt = commands.getstatusoutput(cmd)
+      adddrivername = txt[1]
+      print "First Installing model driver: %s" % adddrivername
+      cmd = "cd %s; python Install.py -a %s" % (thisdir,adddrivername)
+      txt = commands.getstatusoutput(cmd)
+      if txt[0] != 0:
+         print firstRunOutput
          print txt[1]
-  if txt[0] != 0: error()
+         error()
-  #
+      else:
+        print txt[1]
+      cmd = "cd %s; python Install.py -a %s" % (thisdir,addmodelname)
+      txt = commands.getstatusoutput(cmd)
+      print txt[1]
+      if txt[0] != 0:
+        error()
+    else:
+      print firstRunOutput
+      error()
+  else:
+
+    # success
+
+    print firstRunOutput
     print "Removing kim item source and build files ..."
     cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname)
     txt = commands.getstatusoutput(cmd)

lib/kim/README

@@ -8,14 +8,16 @@ James Sethna (Cornell U).  Ryan Elliott is the main developer for the
 KIM API and he also maintains the code that implements the pair_style
 kim command.
 
-To download, build, and install the KIM API on your system, follow
+You can type "make lib-kim" from the src directory to see help on
-these steps.  You can use the install.py script to automate these steps.
+how to download and build this library via make commands, or you can
+do the same thing by typing "python Install.py" from within this
+directory, or you can do it manually by following the instructions
+below.
 
 -----------------
 
 Instructions:
 
-
 1. Configure lammps for use with the kim-api library installed in this directory
 
 $ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
@@ -65,7 +67,7 @@ $ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
 When these steps are complete you can build LAMMPS with the KIM
 package installed:
 
-$ cd ../../src
+$ cd lammpos/src
 $ make yes-kim
 $ make g++ (or whatever target you wish)
 

lib/linalg/Install.py

@@ -8,9 +8,15 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine
+Syntax from src dir: make lib-linalg args="-m machine"
+Syntax from lib dir: python Install.py -m machine
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
+
+Example:
+
+make lib-linalg args="-m gfortran"   # build with GNU Fortran compiler
 """
 
 # print error message or help

lib/meam/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/mscg/Install.py

@@ -8,8 +8,11 @@ import sys,os,re,commands
 # help message
 
 help = """
-Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
+Syntax from src dir: make lib-mscg args="-h hpath hdir -g -b [suffix] -l"
+Syntax from lib dir: python Install.py -h hpath hdir -g -b [suffix] -l
+
 specify one or more options, order does not matter
+
   -h = set home dir of MS-CG to be hpath/hdir
        hpath can be full path, contain '~' or '.' chars
        default hpath = . = lib/mscg
@@ -22,6 +25,10 @@ Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
        optional suffix specifies which src/Make/Makefile.suffix to use
        default suffix = g++_simple
   -l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir
+
+Example:
+
+make lib-mscg args="-g -b -l"   # download/build in lib/mscg/MSCG-release-master
 """
 
 # settings

lib/poems/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/qmmm/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/reax/Install.py

@@ -9,12 +9,21 @@ import sys,commands,os
 # help message
 
 help = """
-Syntax: python Install.py -m machine -e suffix
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
+
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
+
+Examplesx:
+
+make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort"      # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help

lib/smd/Install.py

@@ -8,8 +8,11 @@ import sys,os,re,glob,commands
 # help message
 
 help = """
-Syntax: python Install.py -h hpath hdir -g -l
+Syntax from src dir: make lib-smd args="-h hpath hdir -g -l"
+Syntax from lib dir: python Install.py -h hpath hdir -g -l
+
 specify one or more options, order does not matter
+
   -h = set home dir of Eigen to be hpath/hdir
        hpath can be full path, contain '~' or '.' chars
        default hpath = . = lib/smd
@@ -19,6 +22,10 @@ Syntax: python Install.py -h hpath hdir -g -l
        hpath must already exist
        if hdir already exists, it will be deleted before unpack
   -l = create softlink (includelink) in lib/smd to Eigen src dir
+
+Example:
+
+make lib-smd args="-g -l"   # download/build in default lib/smd/eigen-eigen-*
 """
 
 # settings

lib/voronoi/Install.py

@@ -8,8 +8,11 @@ import sys,os,re,urllib,commands
 # help message
 
 help = """
-Syntax: python Install.py -v version -h hpath hdir -g -b -l
+Syntax from src dir: make lib-voronoi args="-v version -h hpath hdir -g -b -l"
+Syntax from lib dir: python Install.py -v version -h hpath hdir -g -b -l
+
 specify one or more options, order does not matter
+
   -v = version of Voro++ to download and build
        default version = voro++-0.4.6 (current as of Jan 2015)
   -h = set home dir of Voro++ to be hpath/hdir
@@ -22,6 +25,10 @@ Syntax: python Install.py -v version -h hpath hdir -g -b -l
        if hdir already exists, it will be deleted before unpack
   -b = build Voro++ library in its src dir
   -l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir
+
+Example:
+
+make lib-voronoi args="-g -b -l"   # download/build in lib/voronoi/voro++-0.4.6
 """
 
 # settings

src/Makefile

@@ -116,7 +116,8 @@ help:
 	@echo 'make package-overwrite   replace package files with src files'
 	@echo 'make package-diff (pd)   diff src files against package files'
 	@echo ''
-	@echo 'make lib-package         download/build/install a package library'
+	@echo 'make lib-package         help for download/build/install a package library'
+	@echo 'make lib-package args="..."    download/build/install a package library'
 	@echo 'make purge               purge obsolete copies of source files'
 	@echo ''
 	@echo 'make machine             build LAMMPS for machine'