diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt
index 26dc3b96985afbf2c3fe7956d7f395b66be07229..f8b39be1738c46a31ba27d37bbb1af62ab3d9bf9 100644
--- a/doc/src/Section_example.txt
+++ b/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
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 76f88b8ab81967f53e9dd96cb6402bb7dbcbc5e2..a65e510654c64670230210da4139689871c09237 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -492,14 +492,38 @@ Minnesota).
[Install or un-install:]
-Using this package requires the KIM library and its models
-(interatomic potentials) to be downloaded and installed on your
-system. The library can be downloaded and built in lib/kim or
-elsewhere on your system. Details of the download, build, and install
-process for KIM are given in the lib/kim/README file.
+Before building LAMMPS with this package, you must first download and
+build the KIM library and include the KIM models that you want to
+use. You can do this manually if you prefer; follow the instructions
+in lib/kim/README. You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/kim/Install.py script with the specified args.
+
+make lib-kim # print help message
+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
-Once that process is complete, you can then install/un-install the
-package and build LAMMPS in the usual manner:
+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="-h . eigen -g -l" # download in lib/smd/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 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
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index 5c149d892ddbbc2d35be8af744d1beab3f812e27..c4544cb29bde3ccf25b708e7d2ad552fc97e7eea 100644
--- a/doc/src/neigh_modify.txt
+++ b/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 =
-2000, and binsize = 0.0.
+cluster = no, include = all (same as no include option defined),
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.
diff --git a/examples/README b/examples/README
index e4312e25981766183a5a3f0a10c5dfd3f9e523c4..0ec28aa2c259f4df887f24d2f4d0a92e01f5deb0 100644
--- a/examples/README
+++ b/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
diff --git a/lib/Install.py b/lib/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/Install.py
+++ b/lib/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/atc/Install.py b/lib/atc/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/atc/Install.py
+++ b/lib/atc/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/awpmd/Install.py b/lib/awpmd/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/awpmd/Install.py
+++ b/lib/awpmd/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py
index d396be5e1a00fdbc296d711faaafbd46a3e3a811..c6cd1f3021b117ec7bf0986e685f840cd59e998c 100644
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@@ -8,14 +8,17 @@ 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
- 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
- optionally uses Makefile.auto to build the GPU library -> libgpu.a
- and to copy a Makefile.lammps.esuffix -> Makefile.lammps
- optionally copies Makefile.auto to a new Makefile.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
+optionally uses Makefile.auto to build the GPU library -> libgpu.a
+ and to copy a Makefile.lammps.esuffix -> Makefile.lammps
+optionally copies Makefile.auto to a new Makefile.osuffix
-i = use Makefile.isuffix as starting point, copy to Makefile.auto
default isuffix = linux
@@ -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
diff --git a/lib/h5md/Install.py b/lib/h5md/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/h5md/Install.py
+++ b/lib/h5md/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index bcd22dcbb3dc80300cdd4754bc2064bb7e5d452b..9f36f9fedb1fc7c70deddb99fc5b9a1d892011ac 100644
--- a/lib/kim/Install.py
+++ b/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
- specify one or more options, order does not matter
- -v = version of kim-api to download and work with
- default = kim-api-v1.8.2 (current as of June 2017)
- -c = create Makefile.KIM_DIR within lammps lib/kim to configure lammps
- for use with the kim-api library installed at "kim-dir" (absolute
- path). default = this dir
- -b = build kim-api and kim model where kim-model-name can be a specific
- openkim.org model name (such as
- "EAM_Dynamo_Ackland_W__MO_141627196590_002") or the keyword
- "OpenKIM" to install all compatible models from the openkim.org
- site.
- -a = add kim-name openkim.org item (model driver or model) to existing
- kim-api instalation.
+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 library to use
+ default = kim-api-v1.8.2 (current as of June 2017)
+ -b = download and build KIM API library with KIM models
+ kim-dir = where to install/build the KIM API library
+ use "." to install in lib/kim
+ kim-name = none to install only the example KIM models
+ kim-name = KIM model name (see example below) + examples
+ kim-name = OpenKIM to install all models
+ from the openkim.org site (this can take 30 minutes or more)
+ -a = add single KIM model or model driver with kim-name
+ to existing KIM API lib (see example below)
+
+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()
- modelname = args[iarg+1]
- iarg += 2
+ if iarg+3 > len(args): error()
+ dir = args[iarg+1]
+ 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 buildflag == 1:
+
+ # 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
-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)
+ 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)
-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)
+ # download entire kim-api tarball
+ # try first via urllib
+ # if fails (probably due to no SSL support), use wget
-if buildflag == 1:
- # download kim-api
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)
@@ -109,42 +157,101 @@ 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)
- print txt[1]
- if txt[0] != 0: error()
- #
- 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)
- print txt[1]
- if txt[0] != 0: error()
+ 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]
+ 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)
+ print txt[1]
+ if txt[0] != 0: error()
diff --git a/lib/kim/README b/lib/kim/README
index 00d6ea8fadc296b24a15c41ff831bcec8d6ca698..7a4230dc25e99a282b5ba9b8e439d0b0250da058 100644
--- a/lib/kim/README
+++ b/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
-these steps. You can use the install.py script to automate these steps.
+You can type "make lib-kim" from the src directory to see help on
+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)
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
index c7076ca52f28dd63d09dae244f8491110d4a7891..560afecec42a844184b6723f1f87c55177cfd768 100644
--- a/lib/linalg/Install.py
+++ b/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
diff --git a/lib/meam/Install.py b/lib/meam/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/meam/Install.py
+++ b/lib/meam/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py
index e54723261452d1af2ddf1c837985089fd71aa2cd..7b10be189fee9b5c60fb84d318dcf388fb510926 100644
--- a/lib/mscg/Install.py
+++ b/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
- specify one or more options, order does not matter
+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
diff --git a/lib/poems/Install.py b/lib/poems/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/poems/Install.py
+++ b/lib/poems/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/qmmm/Install.py b/lib/qmmm/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/qmmm/Install.py
+++ b/lib/qmmm/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/reax/Install.py b/lib/reax/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..29270560a6a9711150eafcd9bb5daf7bf7c725fe 100644
--- a/lib/reax/Install.py
+++ b/lib/reax/Install.py
@@ -9,12 +9,21 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+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
diff --git a/lib/smd/Install.py b/lib/smd/Install.py
index dc0a3187ce546e81176d780297588a91b04dccce..e6fe8926a46621002c28e4e85f02598142435fa3 100644
--- a/lib/smd/Install.py
+++ b/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
- specify one or more options, order does not matter
+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
diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py
index 7d847183b38fb3e0733df56f33a4ccffcf479bbc..54246f113e3f0a87ff7f093da08a1a500be197d4 100644
--- a/lib/voronoi/Install.py
+++ b/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
- specify one or more options, order does not matter
+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
diff --git a/src/Makefile b/src/Makefile
index c7b20dcb1301803f84b4baabf62e1004ea670d5f..3d1085e0be5c0a5bda16580dc60a0a6ce5474f8c 100644
--- a/src/Makefile
+++ b/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'