From 236241b100850ff9f3a256bfbb4d7c5c6ab4cf45 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 27 Aug 2016 23:09:15 +0000
Subject: [PATCH] sync with Git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15518 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Makefile | 2 +-
doc/README.md | 20 +-
doc/html/fix_nve_manifold_rattle.html | 7 +-
doc/html/fix_nvt_manifold_rattle.html | 7 +-
doc/src/fix_nve_manifold_rattle.txt | 6 +-
doc/src/fix_nvt_manifold_rattle.txt | 6 +-
doc/utils/sha1sum.py | 7 +
src/COMPRESS/Install.sh | 4 +
src/CORESHELL/Install.sh | 4 +
src/Depend.sh | 4 +
src/GPU/Install.sh | 4 +
src/Install.sh | 4 +
src/KIM/Install.sh | 4 +
src/KOKKOS/Install.sh | 4 +
src/MEAM/Install.sh | 4 +
src/MPIIO/Install.sh | 4 +
src/Make.py | 365 +++++++++++++-------------
src/Make.sh | 6 +
src/OPT/Install.sh | 4 +
src/POEMS/Install.sh | 4 +
src/PYTHON/Install.sh | 4 +
src/Package.sh | 4 +
src/REAX/Install.sh | 4 +
src/USER-ATC/Install.sh | 4 +
src/USER-AWPMD/Install.sh | 4 +
src/USER-CG-CMM/Install.sh | 4 +
src/USER-COLVARS/Install.sh | 4 +
src/USER-FEP/Install.sh | 8 +-
src/USER-H5MD/Install.sh | 4 +
src/USER-INTEL/Install.sh | 4 +
src/USER-MISC/Install.sh | 4 +
src/USER-MOLFILE/Install.sh | 4 +
src/USER-OMP/Install.sh | 4 +
src/USER-PHONON/Install.sh | 4 +
src/USER-QMMM/Install.sh | 4 +
src/USER-QUIP/Install.sh | 4 +
src/USER-SMD/Install.sh | 4 +
src/USER-VTK/Install.sh | 4 +
src/VORONOI/Install.sh | 4 +
39 files changed, 353 insertions(+), 197 deletions(-)
create mode 100755 doc/utils/sha1sum.py
diff --git a/doc/Makefile b/doc/Makefile
index 198fffda22..8ee8379c58 100644
--- a/doc/Makefile
+++ b/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
diff --git a/doc/README.md b/doc/README.md
index fb130b35b9..26a51c13ab 100644
--- a/doc/README.md
+++ b/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.
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 3f7633ded4..dbcf0a2488 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/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>
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index 35e6ea6135..98dd612247 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/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>
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index a35c234e63..8d0eb8e57c 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/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/.
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index 42a06d4ed7..f117d10eb9 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/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/.
diff --git a/doc/utils/sha1sum.py b/doc/utils/sha1sum.py
new file mode 100755
index 0000000000..d4842ecf1a
--- /dev/null
+++ b/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())
diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh
index 49bc09f709..ef1c8920c8 100644
--- a/src/COMPRESS/Install.sh
+++ b/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 () {
diff --git a/src/CORESHELL/Install.sh b/src/CORESHELL/Install.sh
index 871a78ca88..f5ea54ac86 100644
--- a/src/CORESHELL/Install.sh
+++ b/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 () {
diff --git a/src/Depend.sh b/src/Depend.sh
index 698c165233..7eb485cb1d 100644
--- a/src/Depend.sh
+++ b/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
diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index 0ff436e95d..ca73adbf82 100644
--- a/src/GPU/Install.sh
+++ b/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 () {
diff --git a/src/Install.sh b/src/Install.sh
index 322631fce9..307188a09f 100644
--- a/src/Install.sh
+++ b/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 () {
diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh
index 128cf1585a..bac9d97cc6 100644
--- a/src/KIM/Install.sh
+++ b/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 () {
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index 80a1bb8df0..c269de41d3 100644
--- a/src/KOKKOS/Install.sh
+++ b/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 () {
diff --git a/src/MEAM/Install.sh b/src/MEAM/Install.sh
index acf4c90910..1825d4327f 100644
--- a/src/MEAM/Install.sh
+++ b/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 () {
diff --git a/src/MPIIO/Install.sh b/src/MPIIO/Install.sh
index 08d284dd2e..3834aea5c5 100644
--- a/src/MPIIO/Install.sh
+++ b/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 () {
diff --git a/src/Make.py b/src/Make.py
index 81f3060c21..0fb2980823 100755
--- a/src/Make.py
+++ b/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 = 0, print str as warning and do not exit
+# if flag = 1, print txt and 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)
- txt = commands.getoutput(str)
+ tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
+ 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
- if txt: print txt
- else: print "compile produced no output"
+ print(tmp)
+ if txt: print(txt)
+ 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)
- txt = commands.getoutput(str)
+ tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
+ 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
- if txt: print txt
- else: print "link produced no output"
+ print(tmp)
+ if txt: print(txt)
+ 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 ..."
- str = "%s.build()" % suffix
- exec(str)
+ print("building",suffix,"library ...")
+ txt = "%s.build()" % suffix
+ 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 ..."
- str = "%s.build()" % pkg
- exec(str)
+ print("building",pkg,"library ...")
+ txt = "%s.build()" % pkg
+ 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
- commands.getoutput(str)
- print "Performed make clean-auto"
+ txt = "cd %s; make clean-auto" % dir.src
+ subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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 ..."
- str = "cd %s/STUBS; make clean; make" % dir.src
- txt = commands.getoutput(str)
+ print("building serial STUBS library ...")
+ tmp = "cd %s/STUBS; make clean; make" % dir.src
+ 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)
- else: str = "cd %s; %s auto" % (dir.src,make)
+ if jmake: tmp = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
+ 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
- try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
- except Exception as e: print e.output
+ print(tmp)
+ try: subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True)
+ 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
- output = commands.getoutput(str).split('\n')
+ tmp = "cd %s; make ps" % dir.src
+ 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)
- print "Package status after installation:"
- print txt
+ txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
+ print("Package status after installation:")
+ 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 ..."
- commands.getoutput("cd %s; make no-all" % dir.src)
+ print("Restoring packages to original state ...")
+ 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)
- print "Restored package status:"
- print txt
+ txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
+ print("Restored package status:")
+ 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:]))
- else: commands.append(line)
+ if label: subprocess.append(' '.join(words[1:]))
+ 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)
- if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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))
- if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
- else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
+ subprocess.check_output("cd %s; %s -f Makefile.auto clean" % (libdir,make),stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- str = "cd %s; make" % libdir
+ subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- else: str = "cd %s; make -f Makefile.auto" % libdir
+ if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+ 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)
- except Exception as e: print e.output
+ try: subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- if verbose: print txt
- print "Created lib/voronoi library"
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True).decode()
+ if verbose: print(txt)
+ 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()
@@ -2310,35 +2313,35 @@ 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)
- print "Created lmp_%s in %s" % (output.machine,dir.cwd)
+ subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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
-
+
if zoutput and actions and \
("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)
- print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
+ subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ 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)
- print "Created Makefile_gpu.%s in %s/MAKE/MINE" % \
- (zoutput.machine,dir.src)
+ subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ print("Created Makefile_gpu.%s in %s/MAKE/MINE" % \
+ (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)
- print "Created Makefile_gpu_lammps.%s in %s/MAKE/MINE" % \
- (zoutput.machine,dir.src)
+ subprocess.check_output(txt,stderr=subprocess.STDOUT,shell=True)
+ print("Created Makefile_gpu_lammps.%s in %s/MAKE/MINE" % \
+ (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 >>fp,switch2str(switches,switch_order)
+ print("# last invoked Make.py command", file=fp)
+ print(switch2str(switches,switch_order), file=fp)
fp.close()
# if not redoflag, done
diff --git a/src/Make.sh b/src/Make.sh
index 3332be92c4..fbed1a8bcd 100644
--- a/src/Make.sh
+++ b/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
diff --git a/src/OPT/Install.sh b/src/OPT/Install.sh
index 2374072a69..ca1231c615 100644
--- a/src/OPT/Install.sh
+++ b/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
diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh
index b03792e4f1..7996f542be 100644
--- a/src/POEMS/Install.sh
+++ b/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
diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh
index 02c7acc812..3d6f71958a 100755
--- a/src/PYTHON/Install.sh
+++ b/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
diff --git a/src/Package.sh b/src/Package.sh
index 80677665eb..ce3819b590 100644
--- a/src/Package.sh
+++ b/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
diff --git a/src/REAX/Install.sh b/src/REAX/Install.sh
index af0f1e2436..f0083810e9 100644
--- a/src/REAX/Install.sh
+++ b/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
diff --git a/src/USER-ATC/Install.sh b/src/USER-ATC/Install.sh
index 03ec562a6a..1137389018 100755
--- a/src/USER-ATC/Install.sh
+++ b/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
diff --git a/src/USER-AWPMD/Install.sh b/src/USER-AWPMD/Install.sh
index 6fd0718b71..7922c53395 100644
--- a/src/USER-AWPMD/Install.sh
+++ b/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
diff --git a/src/USER-CG-CMM/Install.sh b/src/USER-CG-CMM/Install.sh
index 8e4376e961..00f515b794 100644
--- a/src/USER-CG-CMM/Install.sh
+++ b/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
diff --git a/src/USER-COLVARS/Install.sh b/src/USER-COLVARS/Install.sh
index d4e252c223..c01719e766 100755
--- a/src/USER-COLVARS/Install.sh
+++ b/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
diff --git a/src/USER-FEP/Install.sh b/src/USER-FEP/Install.sh
index 695d2baf69..09c2024ad2 100644
--- a/src/USER-FEP/Install.sh
+++ b/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 () {
diff --git a/src/USER-H5MD/Install.sh b/src/USER-H5MD/Install.sh
index 32bd9d1931..bdda732807 100644
--- a/src/USER-H5MD/Install.sh
+++ b/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 () {
diff --git a/src/USER-INTEL/Install.sh b/src/USER-INTEL/Install.sh
index 5b7e9e40b3..79cc1158e9 100644
--- a/src/USER-INTEL/Install.sh
+++ b/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 () {
diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh
index 8b2e864787..203d923164 100644
--- a/src/USER-MISC/Install.sh
+++ b/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 () {
diff --git a/src/USER-MOLFILE/Install.sh b/src/USER-MOLFILE/Install.sh
index df193a6f44..19fd3bd361 100644
--- a/src/USER-MOLFILE/Install.sh
+++ b/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 () {
diff --git a/src/USER-OMP/Install.sh b/src/USER-OMP/Install.sh
index 85b44f1bee..bb4ef6c3aa 100644
--- a/src/USER-OMP/Install.sh
+++ b/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 () {
diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh
index 36cd17daae..cfa369bb05 100644
--- a/src/USER-PHONON/Install.sh
+++ b/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 () {
diff --git a/src/USER-QMMM/Install.sh b/src/USER-QMMM/Install.sh
index 02efdf2d7e..089b880a77 100755
--- a/src/USER-QMMM/Install.sh
+++ b/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 () {
diff --git a/src/USER-QUIP/Install.sh b/src/USER-QUIP/Install.sh
index 9cc672aefa..ee7faaf62a 100644
--- a/src/USER-QUIP/Install.sh
+++ b/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 () {
diff --git a/src/USER-SMD/Install.sh b/src/USER-SMD/Install.sh
index 4cc736e96d..c0f48c5460 100644
--- a/src/USER-SMD/Install.sh
+++ b/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 () {
diff --git a/src/USER-VTK/Install.sh b/src/USER-VTK/Install.sh
index d61e0640f9..d02dc87772 100644
--- a/src/USER-VTK/Install.sh
+++ b/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 () {
diff --git a/src/VORONOI/Install.sh b/src/VORONOI/Install.sh
index a93b2cab7e..f21e9404eb 100755
--- a/src/VORONOI/Install.sh
+++ b/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 () {
--
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