add code and scripts to support all three plumed linkage modes with fix plumed... (04520e62) · Commits · 郑智淋 / lammps

lib/plumed/Install.py

+17 −19

Original line number	Diff line number	Diff line
		@@ -11,27 +11,29 @@ import sys,os,re,subprocess,hashlib
		help = """
		Syntax from src dir: make lib-plumed args="-b"
		or: make lib-plumed args="-b -v 2.4.3"
		or: make lib-plumed args="-p /usr/local/plumed2-2.4.3"
		or: make lib-plumed args="-p /usr/local/plumed2 -m shared"

		Syntax from lib dir: python Install.py -b -v 2.4.3
		or: python Install.py -b
		or: python Install.py -p /usr/local/plumed2-2.4.3
		or: python Install.py -p /usr/local/plumed2 -m shared

		specify one or more options, order does not matter

		-b = download and build the plumed2 library
		-p = specify folder of existing plumed2 installation
		-v = set version of plumed2 to download and build (default: 2.4.3)
		-p = specify folder of existing plumed2 installation
		-m = set plumed linkage mode: static (default), shared, or runtime

		Example:

		make lib-plumed args="-b" # download/build in lib/plumed/plumed2
		make lib-plumed args="-p $HOME/plumed-2.4.3" # use existing Plumed2 installation in $HOME/plumed-2.4.3
		make lib-plumed args="-p $HOME/plumed2 -m shared" # use existing Plumed2 installation in $HOME/plumed2
		"""

		# settings

		version = "2.4.3"
		mode = "static"

		# known checksums for different PLUMED versions. used to validate the download.
		checksums = { \
		@@ -40,11 +42,6 @@ checksums = { \
		'2.5b' : 'e341bdef469be1da058b8a0b97a3db22', \
		}

		#checksums = { \
		# '2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
		# '2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
		# }

		# print error message or help
		def error(str=None):
		if not str: print(help)
		@@ -132,6 +129,10 @@ while iarg < nargs:
		plumedpath = fullpath(args[iarg+1])
		pathflag = True
		iarg += 2
		elif args[iarg] == "-m":
		if iarg+2 > nargs: error()
		mode = args[iarg+1]
		iarg += 2
		elif args[iarg] == "-b":
		buildflag = True
		iarg += 1
		@@ -149,13 +150,14 @@ if (buildflag and pathflag):
		if (not buildflag and not pathflag):
		error("Have to use either -b or -p flag")

		if ((mode != "static") and (mode != "shared") and (mode != "runtime")):
		error("Unknown linkage mode '%s' for Plumed" % mode)

		# download and unpack plumed2 tarball

		if buildflag:
		url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
		filename = "plumed-src-%s.tar.gz" %version
		#url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
		#filename = "v%s.tar.gz" %version
		print("Downloading plumed ...")
		geturl(url,filename)

		@@ -168,9 +170,6 @@ if buildflag:
		if os.path.exists("%s/plumed-%s" % (homepath,version)):
		cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		#if os.path.exists("%s/plumed2-%s" % (homepath,version)):
		# cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
		# subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if os.path.exists("%s/plumed2" % (homepath)):
		cmd = 'rm -rf "%s/plumed2"' % (homepath)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		@@ -183,7 +182,6 @@ if buildflag:
		if buildflag:
		print("Building plumed ...")
		cmd = 'cd %s/plumed-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
		#cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		print(txt.decode('UTF-8'))
		#
		@@ -195,12 +193,12 @@ if linkflag:
		os.remove("includelink")
		if os.path.isfile("liblink") or os.path.islink("liblink"):
		os.remove("liblink")
		cmd = 'ln -s "%s/plumed2/include" includelink' % homepath
		cmd = 'ln -s "%s/include" includelink' % homedir
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		cmd = 'ln -s "%s/plumed2/lib" liblink' % homepath
		cmd = 'ln -s "%s/lib" liblink' % homedir
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if os.path.isfile("Makefile.lammps.static"):
		if os.path.isfile("Makefile.lammps.%s" % mode):
		print("Creating Makefile.lammps")
		cmd = 'cat liblink/plumed/src/lib/Plumed.inc.static Makefile.lammps.static > Makefile.lammps'
		cmd = 'echo PLUMED_LIBDIR="%s/lib" > Makefile.lammps; cat liblink/plumed/src/lib/Plumed.inc.%s Makefile.lammps.%s >> Makefile.lammps' % (homedir,mode,mode)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

lib/plumed/Makefile.lammps.runtime

0 → 100644

+5 −0

Original line number	Diff line number	Diff line
		# Settings that the LAMMPS build will import when this package library is used

		plumed_SYSINC = -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=$(PLUMED_LIBDIR)/libplumedKernel.so
		plumed_SYSLIB = $(PLUMED_LOAD) -rdynamic
		plumed_SYSPATH =

lib/plumed/Makefile.lammps.shared

0 → 100644

+5 −0

Original line number	Diff line number	Diff line
		# Settings that the LAMMPS build will import when this package library is used

		plumed_SYSINC =
		plumed_SYSLIB = $(PLUMED_LOAD)
		plumed_SYSPATH =

lib/plumed/Makefile.lammps.static

+3 −1

Original line number	Diff line number	Diff line
		# Settings that the LAMMPS build will import when this package library is used

		plumed_SYSINC =
		# Use statically linked C++ interface to plumed

		plumed_SYSINC = -D__PLUMED_WRAPPER_CXX=1
		plumed_SYSLIB = $(PLUMED_LOAD)
		plumed_SYSPATH =

src/USER-PLUMED/fix_plumed.cpp

+11 −5

Original line number	Diff line number	Diff line
		@@ -34,13 +34,14 @@
		#include "modify.h"
		#include "pair.h"

		/*
		Use statically linked C++ interface to plumed
		*/
		#define __PLUMED_WRAPPER_CXX 1

		#include "plumed/wrapper/Plumed.h"

		#if defined(__PLUMED_DEFAULT_KERNEL)
		#define PLUMED_QUOTE_DIRECT(name) #name
		#define PLUMED_QUOTE(macro) PLUMED_QUOTE_DIRECT(macro)
		static char plumed_default_kernel[] = "PLUMED_KERNEL=" PLUMED_QUOTE(__PLUMED_DEFAULT_KERNEL);
		#endif

		/* -------------------------------------------------------------------- */

		using namespace LAMMPS_NS;
		@@ -64,6 +65,11 @@ FixPlumed::FixPlumed(LAMMPS lmp, int narg, char *arg) :
		error->warning(FLERR,"Fix group for fix plumed is not 'all'. "
		"Group will be ignored.");

		#if defined(__PLUMED_DEFAULT_KERNEL)
		if (getenv("PLUMED_KERNEL") == NULL)
		putenv(plumed_default_kernel);
		#endif

		p=new PLMD::Plumed;

		// Check API version

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