rename USER-SMD package to MACHDYN

lib/machdyn/.gitignore

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+# ignore these entries with git
+/eigen.tar.gz
+/eigen-eigen-*
+/includelink
+/eigen3

lib/machdyn/Install.py

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+#!/usr/bin/env python
+
+"""
+Install.py tool to download, unpack, and point to the Eigen library
+used to automate the steps described in the README file in this dir
+"""
+
+from __future__ import print_function
+import sys, os, glob, shutil, tarfile
+from argparse import ArgumentParser
+
+sys.path.append('..')
+from install_helpers import fullpath, geturl, checkmd5sum
+
+parser = ArgumentParser(prog='Install.py',
+                        description="LAMMPS library build wrapper script")
+
+# settings
+
+version = '3.3.7'
+tarball = "eigen.tar.gz"
+
+# known checksums for different Eigen versions. used to validate the download.
+checksums = { \
+              '3.3.7' : '9e30f67e8531477de4117506fe44669b' \
+}
+
+
+# help message
+
+HELP = """
+Syntax from src dir: make lib-smd args="-b"
+                 or: make lib-smd args="-p /usr/include/eigen3"
+
+Syntax from lib dir: python Install.py -b
+                 or: python Install.py -p /usr/include/eigen3"
+                 or: python Install.py -v 3.3.7 -b
+
+Example:
+
+make lib-smd args="-b"   # download/build in default lib/smd/eigen-eigen-*
+make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
+"""
+
+pgroup = parser.add_mutually_exclusive_group()
+pgroup.add_argument("-b", "--build", action="store_true",
+                    help="download and build the Eigen3 library")
+pgroup.add_argument("-p", "--path",
+                    help="specify folder of existing Eigen installation")
+parser.add_argument("-v", "--version", default=version,
+                    help="set version of Eigen to download and build (default: %s)" % version)
+
+args = parser.parse_args()
+
+# print help message and exit, if neither build nor path options are given
+if not args.build and not args.path:
+  parser.print_help()
+  sys.exit(HELP)
+
+homepath = fullpath(".")
+eigenpath = os.path.join(homepath, "eigen3")
+
+buildflag = args.build
+pathflag = args.path is not None
+version = args.version
+
+if pathflag:
+  eigenpath = args.path
+  if not os.path.isdir(eigenpath):
+    sys.exit("Eigen path %s does not exist" % eigenpath)
+  eigenpath = fullpath(eigenpath)
+
+# download and unpack Eigen tarball
+# use glob to find name of dir it unpacks to
+
+if buildflag:
+  print("Downloading Eigen ...")
+  eigentar = os.path.join(homepath, tarball)
+  url = "https://gitlab.com/libeigen/eigen/-/archive/%s/eigen-%s.tar.gz" %  (version,version)
+  geturl(url, eigentar)
+
+  # verify downloaded archive integrity via md5 checksum, if known.
+  if version in checksums:
+    print("checking version %s\n" % version)
+    if not checkmd5sum(checksums[version], eigentar):
+      sys.exit("Checksum for Eigen library does not match")
+
+
+  print("Cleaning up old folders ...")
+  edir = glob.glob(os.path.join(homepath, "eigen-*"))
+  edir.append(eigenpath)
+  for one in edir:
+    if os.path.isdir(one):
+      shutil.rmtree(one)
+
+  print("Unpacking Eigen tarball ...")
+  if tarfile.is_tarfile(eigentar):
+    tgz = tarfile.open(eigentar)
+    tgz.extractall(path=homepath)
+    os.remove(eigentar)
+  else:
+    sys.exit("File %s is not a supported archive" % eigentar)
+  edir = os.path.join(homepath, "eigen-%s" % version)
+  os.rename(edir, eigenpath)
+
+# create link in lib/smd to Eigen src dir
+
+print("Creating link to Eigen include folder")
+if os.path.isfile("includelink") or os.path.islink("includelink"):
+  os.remove("includelink")
+linkdir = eigenpath
+os.symlink(linkdir, 'includelink')

lib/machdyn/Makefile.lammps

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+# Settings that the LAMMPS build will import when this package library is used
+
+machdyn_SYSINC = -I../../lib/includelink/eigen3
+machdyn_SYSLIB = 
+machdyn_SYSPATH = 

lib/machdyn/README

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+This directory contains links to the Eigen library which is required
+to use the MACHDYN package in a LAMMPS input script.
+
+The Eigen library is available at http://eigen.tuxfamily.org.  It's
+a general C++ template library for linear algebra.
+
+You can type "make lib-smd" from the src directory to see help on how
+to download 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.  Download the Eigen tarball at http://eigen.tuxfamily.org and
+    unpack the tarball either in this /lib/smd directory or somewhere
+    else on your system.  It should unpack with into a directory with
+    a name similar to eigen-eigen-bdd17ee3b1b3.  You can rename
+    the directory to just "eigen" if you wish.  Note that Eigen is a
+    template library, so you do not have to build it.
+
+2.  Create a soft link in this dir (lib/smd)
+    to the eigen directory.  E.g if you unpacked Eigen in this dir:
+      % ln -s eigen-eigen-bdd17ee3b1b3 includelink
+    If you unpacked Eigen somewhere else and renamed
+    the resulting directory to just eigen, then do something like this:
+      % ln -s /home/sjplimp/tools/eigen includelink
+
+When these steps are complete you can build LAMMPS
+with the MACHDYN package installed:
+
+% cd lammps/src
+% make yes-machdyn
+% make g++ (or whatever target you wish)
+
+Note that if you download and unpack a new LAMMPS tarball, the
+"includelink" and "liblink" files will be lost and you will need to
+re-create them (step 2).  If you unpacked the Eigen library in this
+directory (as opposed to somewhere else on your system), you will also
+need to repeat step 1.
+
+The Makefile.lammps file in this directory is there for compatibility
+with the way other libraries under the lib dir are linked with by
+LAMMPS.  However, the Eigen library requires no auxiliary files or
+settings, so its variables are blank.