Added options to link plumed statically

lib/plumed/.gitignore

@@ -0,0 +1,2 @@
+# files to ignore
+/plumed2*

lib/plumed/Install.py

@@ -0,0 +1,147 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, build, and link to the Voro++ library
+# used to automate the steps described in the README file in this dir
+
+from __future__ import print_function
+import sys,os,re,subprocess
+
+# help message
+
+help = """
+Syntax from src dir: make lib-plumed args="-b"
+                 or: make lib-plumed args="-b -v 2.4.2"
+Syntax from lib dir: python Install.py -b -v 2.4.2
+                 or: python Install.py -b
+
+specify one or more options, order does not matter
+
+  -b = download and build the plumed2 library
+  -v = set version of Voro++ to download and build (default: latest stable version)
+
+Example:
+
+make lib-plumed args="-b"   # download/build in lib/plumed/plumed2
+"""
+
+# settings
+
+version = "2.4.2"
+
+# Add known checksums for different PLUMED versions and use them to validate the download
+
+# print error message or help
+def error(str=None):
+  if not str: print(help)
+  else: print("ERROR",str)
+  sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+  return os.path.abspath(os.path.expanduser(path))
+
+def which(program):
+  def is_exe(fpath):
+    return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+  fpath, fname = os.path.split(program)
+  if fpath:
+    if is_exe(program):
+      return program
+  else:
+    for path in os.environ["PATH"].split(os.pathsep):
+      path = path.strip('"')
+      exe_file = os.path.join(path, program)
+      if is_exe(exe_file):
+        return exe_file
+
+  return None
+
+def geturl(url,fname):
+  success = False
+
+  if which('curl') != None:
+    cmd = 'curl -L -o "%s" %s' % (fname,url)
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success and which('wget') != None:
+    cmd = 'wget -O "%s" %s' % (fname,url)
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success:
+    error("Failed to download source code with 'curl' or 'wget'")
+  return
+
+# Here add function to check fsum
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+homepath = "."
+
+buildflag = False
+suffixflag = False
+linkflag = True
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-v":
+    if iarg+2 > nargs: error()
+    version = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-b":
+    buildflag = True
+    iarg += 1
+  else: error()
+
+homepath = fullpath(homepath)
+
+# download and unpack plumed  tarball
+
+if buildflag:
+  url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
+  filename = "v%s.tar.gz" %version
+  print("Downloading plumed  ...")
+  geturl(url,filename) 
+
+  print("Unpacking plumed tarball ...")
+  if os.path.exists("%s/%s" % (homepath,version)):
+    cmd = 'rm -rf "%s/%s"' % (homepath,version)
+    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
+  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  os.remove("%s/v%s.tar.gz" % (homepath,version))
+
+# build plumed
+ 
+if buildflag:
+   print("Building plumed ...")
+   cmd = 'cd %s/plumed2-%s; ./configure ; make' % (homepath,version)
+   txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+   print(txt.decode('UTF-8'))
+# 
+# # create 2 links in lib/voronoi to Voro++ src dir
+# 
+# if linkflag:
+#   print("Creating links to Voro++ include and lib files")
+#   if os.path.isfile("includelink") or os.path.islink("includelink"):
+#     os.remove("includelink")
+#   if os.path.isfile("liblink") or os.path.islink("liblink"):
+#     os.remove("liblink")
+#   cmd = 'ln -s "%s/src" includelink' % homedir
+#   subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+#   cmd = 'ln -s "%s/src" liblink' % homedir
+#   subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

src/USER-PLUMED/Install.sh

@@ -5,20 +5,33 @@ if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's|^PKG_LIB =[ \t]*|& $(PLUMED_LOAD) |' ../Makefile.package
+    if ( ! test -e ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static ) then
         sed -i -e 's|^PKG_SYSINC =[ \t]*|& -D__PLUMED_HAS_DLOPEN |' ../Makefile.package
     fi
+  fi
 
   if (test -e ../Makefile.package.settings) then
+    # This is for statically linking plumed2
+    if ( test -e ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static ) then  
+       fname=`ls ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static` 
+       sed -i -e "4 i \
+include $fname
+" ../Makefile.package.settings
+       dname=`ls ../../lib/plumed/plumed2*/src/wrapper/Plumed.h`
+       ln -s USER-PLUMED/$dname ../Plumed.h
+    # This is for linking plumed2 as a runtime library  -- this is the default behavior
+    else 
     # multiline form needed for BSD sed on Macs
        sed -i -e '4 i \
 PLUMED_LOAD=-ldl
 ' ../Makefile.package.settings
+       cp Plumed.h ..
+       cp Plumed.cpp ..
+    fi
   fi
 
   cp fix_plumed.cpp ..
   cp fix_plumed.h ..
-  cp Plumed.h ..
-  cp Plumed.cpp ..
 
 elif (test $1 = 0) then
 
@@ -28,12 +41,16 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
+    fname=`ls ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static`
+    sed -i -e "\:include $fname: d" ../Makefile.package.settings 
     sed -i -e '/PLUMED_LOAD=-ldl/d' ../Makefile.package.settings
   fi
 
   rm -f ../fix_plumed.cpp
   rm -f ../fix_plumed.h
   rm -f ../Plumed.h
+  if ( test -e ../Plumed.h ) then
        rm -f ../Plumed.cpp
+  fi
 
 fi

src/USER-PLUMED/fix_plumed.cpp

@@ -192,6 +192,9 @@ void FixPlumed::min_setup(int vflag)
 
 void FixPlumed::post_force(int vflag)
 {
+// Check tag is enabled
+  if( !atom->tag_enable ) error->all(FLERR,"to run PLUMED you must have tag_enable==1");
+
   int update_gatindex=0;
 // Try to find out if the domain decomposition has been updated:
   if(nlocal!=atom->nlocal){
@@ -216,10 +219,18 @@ void FixPlumed::post_force(int vflag)
 // In case it has been updated, rebuild the local mass/charges array
 // and tell plumed about the change:
   if(update_gatindex){
-    for(int i=0;i<nlocal;i++){
-      gatindex[i]=atom->tag[i]-1;
-      masses[i]=atom->mass[atom->type[i]];
-      if(atom->q) charges[i]=atom->q[i];
+    for(int i=0;i<nlocal;i++) gatindex[i]=atom->tag[i]-1;
+    // Get masses 
+    if(atom->rmass_flag) {
+       for(int i=0;i<nlocal;i++) masses[i]=atom->rmass[i];
+    } else {
+       for(int i=0;i<nlocal;i++) masses[i]=atom->mass[atom->type[i]];
+    }
+    // Get charges
+    if(atom->q_flag) {
+       for(int i=0;i<nlocal;i++) charges[i]=atom->q[i];
+    } else {
+       for(int i=0;i<nlocal;i++) charges[i]=0.0;
     }
     p->cmd("setAtomsNlocal",&nlocal);
     p->cmd("setAtomsGatindex",gatindex);