sync with Git

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15518 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Makefile

@@ -1,5 +1,5 @@
 # Makefile for LAMMPS documentation
-SHA1          = $(shell echo $USER-$PWD | sha1sum | cut -f1 -d" ")
+SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv

doc/README.md

@@ -15,18 +15,28 @@ make clean-all    # remove entire build folder and any cached data
 ## Installing prerequisites
 
 To run the documention build toolchain Python 3 and virtualenv have to be
-installed. The following are instructions for common Linux distributions:
+installed. Here are instructions for common setups:
 
-### virtualenv
+### Ubuntu
-
-#### Ubuntu
 
 ```bash
 sudo apt-get install python-virtualenv
 ```
 
-#### Fedora
+### Fedora
 
 ```
 sudo yum install python-virtualenv
 ```
+
+### MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from https://www.python.org and install it.
+This will install both Python 3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will
+install virtualenv from the Python Package Index.

doc/html/fix_nve_manifold_rattle.html

@@ -158,7 +158,7 @@ keyword = <em>every</em>
 <p>Perform constant NVE integration to update position and velocity for
 atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
 is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> written out for the special case of
-single-particle constraints as explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
+single-particle constraints as explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
 V is volume; E is energy. This way, the dynamics of particles constrained to
 curved surfaces can be studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this generates
 Brownian motion of particles constrained to a curved surface. For a list of currently supported
@@ -191,6 +191,9 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
 <p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
 was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
 section for more info.</p>
+<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
+will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
+incompatible but no error.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="related-commands">
@@ -199,7 +202,7 @@ section for more info.</p>
 <p><strong>Default:</strong> every = 0, tchain = 3</p>
 <hr class="docutils" />
 <p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
 preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
 </div>
 </div>

doc/html/fix_nvt_manifold_rattle.html

@@ -157,7 +157,7 @@ keyword = <em>temp</em> or <em>tchain</em> or <em>every</em>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
+<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
 canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
 For a list of currently supported manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a></p>
 </div>
@@ -176,6 +176,9 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
 <p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
 was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
 section for more info.</p>
+<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
+will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
+incompatible but no error.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="related-commands">
@@ -184,7 +187,7 @@ section for more info.</p>
 <strong>Default:</strong> every = 0</p>
 <hr class="docutils" />
 <p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
 preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
 </div>
 </div>

doc/src/fix_nve_manifold_rattle.txt

@@ -76,6 +76,10 @@ This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
 was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
 section for more info.
 
+Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
+will not be satisfied very well at all. A warning is generated if the {min_style} is
+incompatible but no error.
+
 :line
 
 [Related commands:]
@@ -90,7 +94,7 @@ section for more info.
 [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
 
 :link(Paquay)
-[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).
+[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
 preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
 
 

doc/src/fix_nvt_manifold_rattle.txt

@@ -62,6 +62,10 @@ This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
 was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
 section for more info.
 
+Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
+will not be satisfied very well at all. A warning is generated if the {min_style} is
+incompatible but no error.
+
 :line
 
 
@@ -76,6 +80,6 @@ section for more info.
 [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
 
 :link(Paquay)
-[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).
+[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
 preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
 

doc/utils/sha1sum.py

@@ -0,0 +1,7 @@
+#!/bin/env python
+# simple utility which reimplements sha1sum using Python
+import hashlib
+import sys
+s = hashlib.sha1()
+s.update(sys.stdin.read().encode())
+print(s.hexdigest())

src/COMPRESS/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/CORESHELL/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/Depend.sh

@@ -1,6 +1,10 @@
 # Depend.sh = Install/unInstall files due to package dependencies
 # this script is invoked after any package is installed/uninstalled
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # all parent/child package dependencies should be listed below
 # parent package = has files that files in another package derive from
 # child package = has files that derive from files in another package

src/GPU/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/Install.sh

@@ -7,6 +7,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/KIM/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/KOKKOS/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/MEAM/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/MPIIO/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/Make.py

@@ -3,9 +3,10 @@
 # Make.py tool for managing packages and their auxiliary libs,
 #   auto-editing machine Makefiles, and building LAMMPS
 # Syntax: Make.py -h (for help)
-# Notes: needs python 2.7 (not Python 3)
+# Notes: should be compatible with python 2.7 and 3.x thanks to 'futurize'
 
-import sys,os,commands,re,copy,subprocess,platform
+from __future__ import print_function
+import sys,os,re,copy,subprocess,platform
 
 # switch abbrevs
 # switch classes = created class for each switch
@@ -34,15 +35,15 @@ gpubuildflag = 0
 # functions
 # ----------------------------------------------------------------
 
-# if flag = 1, print str and exit
+# if flag = 1, print txt and exit
-# if flag = 0, print str as warning and do not exit
+# if flag = 0, print txt as warning and do not exit
 
-def error(str,flag=1):
+def error(txt,flag=1):
   if flag:
-    print "ERROR:",str
+    print("ERROR:",txt)
     sys.exit()
   else:
-    print "WARNING:",str
+    print("WARNING:",txt)
 
 # store command-line args as sw = dict of key/value
 # key = switch word, value = list of following args
@@ -83,15 +84,15 @@ def switch2str(switches,switch_order):
 
 def compile_check(compiler,ccflags,warn):
   open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
-  str = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
+  tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
-  txt = commands.getoutput(str)
+  txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
   flag = 1
   if txt or not os.path.isfile("tmpauto.o"):
     flag = 0
     if warn:
-      print str
+      print(tmp)
-      if txt: print txt
+      if txt: print(txt)
-      else: print "compile produced no output"
+      else: print("compile produced no output")
   os.remove("tmpauto.cpp")
   if os.path.isfile("tmpauto.o"): os.remove("tmpauto.o")
   return flag
@@ -102,15 +103,15 @@ def compile_check(compiler,ccflags,warn):
 
 def link_check(linker,linkflags,libs,warn):
   open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
-  str = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
+  tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
-  txt = commands.getoutput(str)
+  txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
   flag = 1
   if txt or not os.path.isfile("tmpauto"):
     flag = 0
     if warn:
-      print str
+      print(tmp)
-      if txt: print txt
+      if txt: print(txt)
-      else: print "link produced no output"
+      else: print("link produced no output")
   os.remove("tmpauto.cpp")
   if os.path.isfile("tmpauto"): os.remove("tmpauto")
   return flag
@@ -121,7 +122,7 @@ def link_check(linker,linkflags,libs,warn):
 
 # actions
 
-class Actions:
+class Actions(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     
@@ -229,18 +230,18 @@ class Actions:
   
   def lib(self,suffix):
     if suffix != "all":
-      print "building",suffix,"library ..."
+      print("building",suffix,"library ...")
-      str = "%s.build()" % suffix
+      txt = "%s.build()" % suffix
-      exec(str)
+      exec(txt)
     else:
       final = packages.final
       for one in packages.lib:
         if final[one]:
           if "user" in one: pkg = one[5:]
           else: pkg = one
-          print "building",pkg,"library ..."
+          print("building",pkg,"library ...")
-          str = "%s.build()" % pkg
+          txt = "%s.build()" % pkg
-          exec(str)
+          exec(txt)
 
   # read Makefile.machine
   # if caller = "file", edit via switches
@@ -526,8 +527,10 @@ class Actions:
     # unless caller = "exe" and "file" action already invoked
     
     if caller == "file" or "file" not in self.alist:
+      # make certain that 'MAKE/MINE' folder exists.
+      subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,stderr=subprocess.STDOUT,shell=True)
       make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
-      print "Created src/MAKE/MINE/Makefile.auto"
+      print("Created src/MAKE/MINE/Makefile.auto")
       
     # test full compile and link
     # unless caller = "file" and "exe" action will be invoked later
@@ -545,9 +548,9 @@ class Actions:
   # invoke "make clean-auto" to force clean before build
     
   def clean(self):
-    str = "cd %s; make clean-auto" % dir.src
+    txt = "cd %s; make clean-auto" % dir.src
-    commands.getoutput(str)
+    subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-    print "Performed make clean-auto"
+    print("Performed make clean-auto")
 
   # build LAMMPS using Makefile.auto and -j setting
   # invoke self.file() first, to test makefile compile/link
@@ -556,15 +559,15 @@ class Actions:
     
   def exe(self):
     self.file("exe")
-    commands.getoutput("cd %s; rm -f lmp_auto" % dir.src)
+    subprocess.check_output("cd %s; rm -f lmp_auto" % dir.src,stderr=subprocess.STDOUT,shell=True)
     if self.stubs and not os.path.isfile("%s/STUBS/libmpi_stubs.a" % dir.src):
-      print "building serial STUBS library ..."
+      print("building serial STUBS library ...")
-      str = "cd %s/STUBS; make clean; make" % dir.src
+      tmp = "cd %s/STUBS; make clean; make" % dir.src
-      txt = commands.getoutput(str)
+      txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
       if not os.path.isfile("%s/STUBS/libmpi_stubs.a" % dir.src):
-        print txt
+        print(txt)
         error('Unsuccessful "make stubs"')
-      print "Created src/STUBS/libmpi_stubs.a"
+      print("Created src/STUBS/libmpi_stubs.a")
 
     # special hack for shannon GPU cluster
     # must use "srun make" if on it and building w/ GPU package, else just make
@@ -574,24 +577,24 @@ class Actions:
     if "shannon" == platform.node() and packages.final["gpu"]:
       make = "srun make"
       
-    if jmake: str = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
+    if jmake: tmp = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
-    else: str = "cd %s; %s auto" % (dir.src,make)
+    else: tmp = "cd %s; %s auto" % (dir.src,make)
     
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(tmp,shell=True)
     else:
-      print str
+      print(tmp)
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/lmp_auto" % dir.src):
       error('Unsuccessful "make auto"')
-    elif not output: print "Created src/lmp_auto"
+    elif not output: print("Created src/lmp_auto")
     
 # dir switch
 
-class Dir:
+class Dir(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
       
@@ -625,7 +628,7 @@ class Dir:
 
 # help switch
 
-class Help:
+class Help(object):
   def __init__(self,list): pass
 
   def help(self):
@@ -650,7 +653,7 @@ Syntax: Make.py switch args ...
 
 # jmake switch
   
-class Jmake:
+class Jmake(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
   
@@ -671,7 +674,7 @@ class Jmake:
         
 # makefile switch
 
-class Makefile:
+class Makefile(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
   
@@ -690,7 +693,7 @@ class Makefile:
     
 # output switch
 
-class Output:
+class Output(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
 
@@ -707,7 +710,7 @@ class Output:
 
 # packages switch
   
-class Packages:
+class Packages(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
 
@@ -805,14 +808,14 @@ class Packages:
     # key = package name, value = 1 if currently installed, else 0
 
     original = {}
-    str = "cd %s; make ps" % dir.src
+    tmp = "cd %s; make ps" % dir.src
-    output = commands.getoutput(str).split('\n')
+    output = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
     pattern = "Installed\s+(\w+): package (\S+)"
     for line in output:
       m = re.search(pattern,line)
       if not m: continue
       pkg = m.group(2).lower()
-      if pkg not in all: error('Package list does not math "make ps" results')
+      if pkg not in all: error('Package list does not match "make ps" results')
       if m.group(1) == "NO": original[pkg] = 0      
       elif m.group(1) == "YES": original[pkg] = 1
 
@@ -849,33 +852,33 @@ class Packages:
   # install packages in plist
     
   def install(self):
-    if self.plist: print "Installing packages ..."
+    if self.plist: print("Installing packages ...")
     for one in self.plist:
       if one == "orig": continue
-      commands.getoutput("cd %s; make %s" % (dir.src,one))
+      subprocess.check_output("cd %s; make %s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
     if self.plist and verbose:
-      txt = commands.getoutput("cd %s; make ps" % dir.src)
+      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
-      print "Package status after installation:"
+      print("Package status after installation:")
-      print txt
+      print(txt)
       
   # restore packages to original list if requested
   # order of re-install should not matter matter b/c of Depend.sh
   
   def uninstall(self):
     if not self.plist or self.plist[-1] != "orig": return
-    print "Restoring packages to original state ..."
+    print("Restoring packages to original state ...")
-    commands.getoutput("cd %s; make no-all" % dir.src)
+    subprocess.check_output("cd %s; make no-all" % dir.src,stderr=subprocess.STDOUT,shell=True)
     for one in self.all:
       if self.original[one]:
-        commands.getoutput("cd %s; make yes-%s" % (dir.src,one))
+        subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
     if verbose:
-      txt = commands.getoutput("cd %s; make ps" % dir.src)
+      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
-      print "Restored package status:"
+      print("Restored package status:")
-      print txt
+      print(txt)
       
 # redo switch
     
-class Redo:
+class Redo(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
   
@@ -940,8 +943,8 @@ class Redo:
       if words[0][-1] == ':': label = words[0][:-1]
       else: label = None
       if not self.labels:
-        if label: commands.append(' '.join(words[1:]))
+        if label: subprocess.append(' '.join(words[1:]))
-        else: commands.append(line)
+        else: subprocess.append(line)
       else:
         if not label: continue
         dict[label] = ' '.join(words[1:])
@@ -950,13 +953,13 @@ class Redo:
         
     for label in self.labels:
       if label not in dict: error("Redo label not in redo file")
-      commands.append(dict[label])
+      subprocess.append(dict[label])
 
     self.commands = commands
 
 # settings switch
 
-class Settings:
+class Settings(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
   
@@ -979,7 +982,7 @@ class Settings:
   
 # verbose switch
 
-class Verbose:
+class Verbose(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
   
@@ -995,7 +998,7 @@ class Verbose:
 
 # zoutput switch for making copy of final Makefile.auto
 
-class Zoutput:
+class Zoutput(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
 
@@ -1018,7 +1021,7 @@ class Zoutput:
 
 # ATC lib
 
-class ATC:
+class ATC(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "g++"
@@ -1051,25 +1054,25 @@ class ATC:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
     
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
     
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libatc.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/atc library")
-    else: print "Created lib/atc library"
+    else: print("Created lib/atc library")
     
 # AWPMD lib
 
-class AWPMD:
+class AWPMD(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "mpicc"
@@ -1102,25 +1105,25 @@ class AWPMD:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
    
     if not os.path.isfile("%s/libawpmd.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/awpmd library")
-    else: print "Created lib/awpmd library"
+    else: print("Created lib/awpmd library")
 
 # COLVARS lib
 
-class COLVARS:
+class COLVARS(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "g++"
@@ -1153,25 +1156,25 @@ class COLVARS:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libcolvars.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/colvars library")
-    else: print "Created lib/colvars library"
+    else: print("Created lib/colvars library")
 
 # CUDA lib
 
-class CUDA:
+class CUDA(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.mode = "double"
@@ -1205,30 +1208,30 @@ class CUDA:
           
   def build(self): 
     libdir = dir.lib + "/cuda"
-    commands.getoutput("cd %s; make clean" % libdir)
+    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
     if self.mode == "double": n = 2
     elif self.mode == "mixed": n = 3
     elif self.mode == "single": n = 1
-    if jmake: str = "cd %s; make -j %d precision=%d arch=%s" % \
+    if jmake: txt = "cd %s; make -j %d precision=%d arch=%s" % \
           (libdir,jmake.n,n,self.arch)
-    else: str = str = "cd %s; make precision=%d arch=%s" % \
+    else: txt = "cd %s; make precision=%d arch=%s" % \
           (libdir,n,self.arch)
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/liblammpscuda.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/cuda library")
-    else: print "Created lib/cuda library"
+    else: print("Created lib/cuda library")
 
 # GPU lib
 
-class GPU:
+class GPU(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "linux.double"
@@ -1300,25 +1303,25 @@ class GPU:
     make = "make"
     if "shannon" == platform.node(): make = "srun make"
 
-    commands.getoutput("cd %s; %s -f Makefile.auto clean" % (libdir,make))
+    subprocess.check_output("cd %s; %s -f Makefile.auto clean" % (libdir,make),stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
+    if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
-    else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
+    else: txt = "cd %s; %s -f Makefile.auto" % (libdir,make)
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libgpu.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/gpu library")
-    else: print "Created lib/gpu library"
+    else: print("Created lib/gpu library")
 
 # H5MD lib
 
-class H5MD:
+class H5MD(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "h5cc"
@@ -1351,24 +1354,24 @@ class H5MD:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make clean" % libdir)
+    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    str = "cd %s; make" % libdir
+    txt = "cd %s; make" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libch5md.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/h5md library")
-    else: print "Created lib/h5md library"
+    else: print("Created lib/h5md library")
 
 # MEAM lib
 
-class MEAM:
+class MEAM(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "gfortran"
@@ -1401,25 +1404,25 @@ class MEAM:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
     # do not use -j for MEAM build, parallel build does not work
-    str = "cd %s; make -f Makefile.auto" % libdir
+    txt = "cd %s; make -f Makefile.auto" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libmeam.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/meam library")
-    else: print "Created lib/meam library"
+    else: print("Created lib/meam library")
 
 # POEMS lib
 
-class POEMS:
+class POEMS(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "g++"
@@ -1452,25 +1455,25 @@ class POEMS:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libpoems.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/poems library")
-    else: print "Created lib/poems library"
+    else: print("Created lib/poems library")
 
 # PYTHON lib
 
-class PYTHON:
+class PYTHON(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "g++"
@@ -1497,15 +1500,15 @@ class PYTHON:
   def build(self):
     libdir = dir.lib + "/python"
     if self.lammpsflag:
-      commands.getoutput("cd %s; cp Makefile.lammps.%s Makefile.lammps" %
+      subprocess.check_output("cd %s; cp Makefile.lammps.%s Makefile.lammps" %
                          (libdir,self.lammps))
     if not os.path.isfile("%s/Makefile.lammps.%s" % (libdir,self.lammps)):
       error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" % self.lammps)
-    else: print "Created lib/python/Makefile.lammps file"
+    else: print("Created lib/python/Makefile.lammps file")
 
 # QMMM lib
 
-class QMMM:
+class QMMM(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "gfortran"
@@ -1538,25 +1541,25 @@ class QMMM:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
    
     if not os.path.isfile("%s/libqmmm.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/qmmm library")
-    else: print "Created lib/qmmm library"
+    else: print("Created lib/qmmm library")
 
 # REAX lib
 
-class REAX:
+class REAX(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "gfortran"
@@ -1590,24 +1593,24 @@ class REAX:
     make.write("%s/Makefile.auto" % libdir)
 
     commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    else: txt = "cd %s; make -f Makefile.auto" % libdir
     
     # if verbose, print output as build proceeds, else only print if fails
 
-    if verbose: subprocess.call(str,shell=True)
+    if verbose: subprocess.call(txt,shell=True)
     else:
-      try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
+      try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      except Exception as e: print e.output
+      except Exception as e: print(e.output)
 
     if not os.path.isfile("%s/libreax.a" % libdir) or \
           not os.path.isfile("%s/Makefile.lammps" % libdir):
       error("Unsuccessful build of lib/reax library")
-    else: print "Created lib/reax library"
+    else: print("Created lib/reax library")
 
 # VORONOI lib
 
-class VORONOI:
+class VORONOI(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.install = ""
@@ -1635,9 +1638,9 @@ class VORONOI:
     if not self.install: return
     libdir = dir.lib + "/voronoi"
     cmd = "cd %s; python install.py %s" % (libdir,self.install)
-    txt = commands.getoutput(cmd)
+    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True).decode()
-    if verbose: print txt
+    if verbose: print(txt)
-    print "Created lib/voronoi library"
+    print("Created lib/voronoi library")
 
 # ----------------------------------------------------------------
 # build classes for intel, kokkos build options
@@ -1645,7 +1648,7 @@ class VORONOI:
 
 # Intel class
 
-class Intel:
+class Intel(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.mode = "cpu"
@@ -1666,7 +1669,7 @@ class Intel:
 
 # Kokkos class
 
-class Kokkos:
+class Kokkos(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.mode = ""
@@ -1688,7 +1691,7 @@ class Kokkos:
 """
 
   def check(self):
-    print self.inlist
+    print(self.inlist)
     if self.inlist != None and len(self.inlist) == 0:
       error("-kokkos args are invalid")
       
@@ -1710,7 +1713,7 @@ class Kokkos:
 
 # Cc class
 
-class Cc:
+class Cc(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.compiler = self.abbrev = ""
@@ -1762,7 +1765,7 @@ class Cc:
 
 # Flags class
 
-class Flags:
+class Flags(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.flags = []
@@ -1803,7 +1806,7 @@ class Flags:
       
 # Mpi class
 
-class Mpi:
+class Mpi(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.style = self.dir = ""
@@ -1837,7 +1840,7 @@ class Mpi:
 
 # Fft class
 
-class Fft:
+class Fft(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.dir = self.incdir = self.libdir = ""
@@ -1877,7 +1880,7 @@ class Fft:
 
 # Jpg class
 
-class Jpg:
+class Jpg(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.on = 1
@@ -1916,7 +1919,7 @@ class Jpg:
 
 # Png class
 
-class Png:
+class Png(object):
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.on = 1
@@ -1958,7 +1961,7 @@ class Png:
 
 # read, tweak, and write a Makefile
 
-class MakeReader:
+class MakeReader(object):
 
   # read a makefile
   # flag = 0 if file is full path name
@@ -2127,14 +2130,14 @@ class MakeReader:
       if not line.isdigit():
         if flag and i == 0:
           line = "# auto = makefile auto-generated by Make.py"
-        print >>fp,line
+        print(line, file=fp)
       else:
         index = int(line)
         name = self.varinfo[index][0]
         txt = self.varinfo[index][1]
         if name not in self.var: continue
         values = self.var[name]
-        print >>fp,"%s%s" % (txt,' '.join(values))
+        print("%s%s" % (txt,' '.join(values)), file=fp)
   
 # ----------------------------------------------------------------
 # main program
@@ -2203,7 +2206,7 @@ while 1:
       switches[switch] = cmd_switches[switch]
 
     argstr = switch2str(switches,switch_order)
-    print "Redo command: Make.py",argstr
+    print("Redo command: Make.py",argstr)
   else:
     switches = cmd_switches
     switch_order = cmd_switch_order
@@ -2246,10 +2249,10 @@ while 1:
 
   if help or (actions and "-h" in actions.inlist) or not switches:
     if not help: help = Help(None)
-    print help.help()
+    print(help.help())
     for switch in switch_order:
       if switch == "h": continue
-      print classes[switch].help()[1:]
+      print(classes[switch].help()[1:])
     sys.exit()
 
   # create needed default classes if not specified with switch
@@ -2298,7 +2301,7 @@ while 1:
 
   if actions:
     for action in actions.alist:
-      print "Action %s ..." % action
+      print("Action %s ..." % action)
       if action.startswith("lib-"): actions.lib(action[4:])
       elif action == "file": actions.file("file")
       elif action == "clean": actions.clean()
@@ -2310,8 +2313,8 @@ while 1:
 
   if output and actions and "exe" in actions.alist:
     txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
-    commands.getoutput(txt)
+    subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-    print "Created lmp_%s in %s" % (output.machine,dir.cwd)
+    print("Created lmp_%s in %s" % (output.machine,dir.cwd))
 
   # create copy of Makefile.auto if requested, and file or exe action performed
   # ditto for library Makefile.auto and Makefile.lammps files
@@ -2320,25 +2323,25 @@ while 1:
         ("file" in actions.alist or "exe" in actions.alist):
     txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
         (dir.src,dir.src,zoutput.machine)
-    commands.getoutput(txt)
+    subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-    print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
+    print("Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src))
     if gpubuildflag:
       txt = "cp %s/gpu/Makefile.auto %s/MAKE/MINE/Makefile_gpu.%s" % \
           (dir.lib,dir.src,zoutput.machine)
-      commands.getoutput(txt)
+      subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      print "Created Makefile_gpu.%s in %s/MAKE/MINE" % \
+      print("Created Makefile_gpu.%s in %s/MAKE/MINE" % \
-          (zoutput.machine,dir.src)
+          (zoutput.machine,dir.src))
       txt = "cp %s/gpu/Makefile.lammps %s/MAKE/MINE/Makefile_gpu_lammps.%s" % \
           (dir.lib,dir.src,zoutput.machine)
-      commands.getoutput(txt)
+      subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
-      print "Created Makefile_gpu_lammps.%s in %s/MAKE/MINE" % \
+      print("Created Makefile_gpu_lammps.%s in %s/MAKE/MINE" % \
-          (zoutput.machine,dir.src)
+          (zoutput.machine,dir.src))
       
   # write current Make.py command to src/Make.py.last
 
   fp = open("%s/Make.py.last" % dir.src,'w')
-  print >>fp,"# last invoked Make.py command"
+  print("# last invoked Make.py command", file=fp)
-  print >>fp,switch2str(switches,switch_order)
+  print(switch2str(switches,switch_order), file=fp)
   fp.close()
   
   # if not redoflag, done

src/Make.sh

@@ -5,6 +5,12 @@
 #         sh Make.sh Makefile.shlib
 #         sh Make.sh Makefile.list
 
+# turn off enforced customizations
+GREP_OPTIONS=
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL GREP_OPTIONS
+
 # function to create one style_*.h file
 # must whack *.d files that depend on style_*.h file,
 # else Make will not recreate them

src/OPT/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/POEMS/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/PYTHON/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/Package.sh

@@ -1,6 +1,10 @@
 # Package.sh = package management, called from Makefile
 # Syntax: sh Package.sh DIR status/update/overwrite/diff
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # package is already installed if any package *.cpp or *.h file is in src
 # else not installed
 

src/REAX/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/USER-ATC/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/USER-AWPMD/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/USER-CG-CMM/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/USER-COLVARS/Install.sh

@@ -5,6 +5,10 @@ mode=$1
 
 # arg1 = file, arg2 = file it depends on
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 action () {
   if (test $mode = 0) then
     rm -f ../$1

src/USER-FEP/Install.sh

@@ -1,12 +1,12 @@
 # Install/unInstall package files in LAMMPS
 # mode = 0/1/2 for uninstall/install/update
 
-# this is default Install.sh for all packages
-# if package has an auxiliary library or a file with a dependency,
-# then package dir has its own customized Install.sh
-
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-H5MD/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-INTEL/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-MISC/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-MOLFILE/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-OMP/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-PHONON/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-QMMM/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-QUIP/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-SMD/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/USER-VTK/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {

src/VORONOI/Install.sh

@@ -3,6 +3,10 @@
 
 mode=$1
 
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
 # arg1 = file, arg2 = file it depends on
 
 action () {