From c3a95c782bd65a027cacd854859b35721af854b5 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 12 May 2016 13:53:40 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15039
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 python/install.py | 30 +++++++++++++++++++-----------
 python/lammps.py  | 16 +++++++++++++++-
 2 files changed, 34 insertions(+), 12 deletions(-)

diff --git a/python/install.py b/python/install.py
index d733273fe7..9308506fd2 100644
--- a/python/install.py
+++ b/python/install.py
@@ -2,16 +2,18 @@
 
 # copy LAMMPS src/liblammps.so and lammps.py to system dirs
 
+from __future__ import print_function
+
 instructions = """
 Syntax: python install.py [-h] [pydir]
         pydir = target dir for lammps.py and liblammps.so
                 default = Python site-packages dir
 """
 
-import sys,os,commands
+import sys,os,shutil
 
 if (len(sys.argv) > 1 and sys.argv[1] == "-h") or len(sys.argv) > 2:
-  print instructions
+  print(instructions)
   sys.exit()
 
 if len(sys.argv) == 2: pydir = sys.argv[1]
@@ -22,18 +24,24 @@ else: pydir = ""
 
 if pydir:
   if not os.path.isdir(pydir):
-    print "ERROR: pydir %s does not exist" % pydir
+    print( "ERROR: pydir %s does not exist" % pydir)
     sys.exit()
   str = "cp ../python/lammps.py %s" % pydir
-  print str
-  outstr = commands.getoutput(str)
-  if len(outstr.strip()): print outstr
+  print(str)
+  try:
+    shutil.copyfile("../python/lammps.py", os.path.join(pydir,'lammps.py') )
+  except shutil.Error:
+    pass # source and destination are identical
+
   str = "cp ../src/liblammps.so %s" % pydir
-  print str
-  outstr = commands.getoutput(str)
+  print(str)
+  try:
+     shutil.copyfile("../src/liblammps.so", os.path.join(pydir,"liblammps.so") )
+  except shutil.Error:
+    pass # source and destination are identical
   sys.exit()
   
-print "installing lammps.py in Python site-packages dir"
+print("installing lammps.py in Python site-packages dir")
 
 os.chdir('../python')                # in case invoked via make in src dir
 
@@ -60,7 +68,7 @@ try:
         data_files = [(get_python_lib(), ["../src/liblammps.so"])])
 except:
   tryuser=True
-  print "Installation into global site-packages dir failed.\nTrying user site dir %s now." % site.USER_SITE
+  print ("Installation into global site-packages dir failed.\nTrying user site dir %s now." % site.USER_SITE)
 
 
 if tryuser:
@@ -75,7 +83,7 @@ if tryuser:
     py_modules = ["lammps"],
     data_files = [(site.USER_SITE, ["../src/liblammps.so"])])
   except: 
-    print "Installation into user site package dir failed.\nGo to ../python and install manually."
+    print("Installation into user site package dir failed.\nGo to ../python and install manually.")
 
 
 
diff --git a/python/lammps.py b/python/lammps.py
index c6a4b6168e..cb818841f2 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -53,7 +53,7 @@ class lammps:
     except:
       if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
       else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
-        
+
     # if no ptr provided, create an instance of LAMMPS
     #   don't know how to pass an MPI communicator from PyPar
     #   but we can pass an MPI communicator from mpi4py v2.0.0 and later
@@ -125,12 +125,15 @@ class lammps:
     return self.lib.lammps_version(self.lmp)
 
   def file(self,file):
+    file = file.encode()
     self.lib.lammps_file(self.lmp,file)
 
   def command(self,cmd):
+    cmd = cmd.encode()
     self.lib.lammps_command(self.lmp,cmd)
 
   def extract_global(self,name,type):
+    name = name.encode()
     if type == 0:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
     elif type == 1:
@@ -140,6 +143,7 @@ class lammps:
     return ptr[0]
 
   def extract_atom(self,name,type):
+    name = name.encode()
     if type == 0:
       self.lib.lammps_extract_atom.restype = POINTER(c_int)
     elif type == 1:
@@ -153,6 +157,7 @@ class lammps:
     return ptr
 
   def extract_compute(self,id,style,type):
+    id = id.encode()
     if type == 0:
       if style > 0: return None
       self.lib.lammps_extract_compute.restype = POINTER(c_double)
@@ -172,6 +177,7 @@ class lammps:
   # double was allocated by library interface function
   
   def extract_fix(self,id,style,type,i=0,j=0):
+    id = ide.encode()
     if style == 0:
       self.lib.lammps_extract_fix.restype = POINTER(c_double)
       ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
@@ -195,6 +201,8 @@ class lammps:
   # memory was allocated by library interface function
   
   def extract_variable(self,name,group,type):
+    name = name.encode()
+    group = group.encode()
     if type == 0:
       self.lib.lammps_extract_variable.restype = POINTER(c_double)
       ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
@@ -218,6 +226,8 @@ class lammps:
   # returns 0 for success, -1 if failed
   
   def set_variable(self,name,value):
+    name = name.encode()
+    value = str(value).encode()
     return self.lib.lammps_set_variable(self.lmp,name,str(value))
 
   # return total number of atoms in system
@@ -228,6 +238,7 @@ class lammps:
   # return vector of atom properties gathered across procs, ordered by atom ID
 
   def gather_atoms(self,name,type,count):
+    name = name.encode()
     natoms = self.lib.lammps_get_natoms(self.lmp)
     if type == 0:
       data = ((count*natoms)*c_int)()
@@ -242,4 +253,7 @@ class lammps:
   # assume vector is of correct type and length, as created by gather_atoms()
 
   def scatter_atoms(self,name,type,count,data):
+    name = name.encode()
     self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
+
+