Loading lib/plumed/.gitignore 0 → 100644 +2 −0 Original line number Diff line number Diff line # files to ignore /plumed2* lib/plumed/Install.py 0 → 100644 +147 −0 Original line number Diff line number Diff line #!/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 +22 −5 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 +15 −4 Original line number Diff line number Diff line Loading @@ -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){ Loading @@ -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); Loading Loading
lib/plumed/.gitignore 0 → 100644 +2 −0 Original line number Diff line number Diff line # files to ignore /plumed2*
lib/plumed/Install.py 0 → 100644 +147 −0 Original line number Diff line number Diff line #!/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 +22 −5 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 +15 −4 Original line number Diff line number Diff line Loading @@ -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){ Loading @@ -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); Loading
