Merge remote-tracking branch 'github/master' into collected-small-changes

# Conflicts:
#	python/lammps/__init__.py
#	python/lammps/core.py

doc/src/Python_install.rst

@@ -377,14 +377,6 @@ make MPI calls directly from Python in your script, if you desire.
 We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
 (aka mpi4py) and you will find installation instruction for it below.
 
-.. note::
-
-   Older LAMMPS versions were also tested with `PyPar <https://github.com/daleroberts/pypar>`_
-   but we can no longer test it, since it does not work with the Python
-   (3.x) versions on our test servers. Since there have been no updates
-   to PyPar visible in its repository since November 2016 we have to assume
-   it is no longer maintained.
-
 Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
 follows:
 

doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html

@@ -65,7 +65,7 @@
           {% elif show_source and has_source and sourcename %}
             <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
           {% endif %}
-          <a href="http://lammps.sandia.gov">Website</a>
+          <a href="https://www.lammps.org">Website</a>
           <a href="Commands_all.html">Commands</a>
         {% endif %}
       </li>

doc/utils/sphinx-config/_themes/lammps_theme/layout.html

@@ -38,10 +38,11 @@
   {% if favicon %}
     <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
   {% endif %}
-  {# CANONICAL URL #}
+
-  {% if theme_canonical_url %}
+  {#- CANONICAL URL #}
-    <link rel="canonical" href="{{ theme_canonical_url }}{{ pagename }}.html"/>
+  {%- if pageurl %}
-  {% endif %}
+    <link rel="canonical" href="{{ pageurl|e }}" />
+  {%- endif -%}
 
   {# JAVASCRIPTS #}
   {%- block scripts %}

doc/utils/sphinx-config/_themes/lammps_theme/theme.conf

@@ -4,7 +4,6 @@ stylesheet = css/theme.css
 pygments_style = default
 
 [options]
-canonical_url =
 analytics_id =
 collapse_navigation = False
 sticky_navigation = False

doc/utils/sphinx-config/conf.py.in

@@ -15,6 +15,7 @@
 
 import sys
 import os
+from datetime import date
 
 has_enchant = False
 try:
@@ -76,7 +77,7 @@ master_doc = 'Manual'
 
 # General information about the project.
 project = 'LAMMPS'
-copyright = '2003-2020 Sandia Corporation'
+copyright = '2003-{} Sandia Corporation'.format(date.today().year)
 
 def get_lammps_version():
     import os
@@ -255,6 +256,8 @@ htmlhelp_basename = 'LAMMPSdoc'
 
 html_permalinks = True
 
+html_baseurl = os.environ.get('LAMMPS_WEBSITE_BASEURL', '')
+
 if 'epub' in sys.argv:
   html_math_renderer = 'imgmath'
 else:

doc/utils/sphinx-config/false_positives.txt

@@ -2631,7 +2631,6 @@ PyLammps
 pymbar
 pymodule
 pymol
-pypar
 pythonic
 pytorch
 pyy

examples/ELASTIC/compliance.py

@@ -8,6 +8,7 @@
 # The units of Cij are whatever was used in log.lammps (usually GPa)
 # The units of Sij are the inverse of that (usually 1/GPa)
 
+from __future__ import print_function
 from numpy import zeros
 from numpy.linalg import inv
 
@@ -44,8 +45,7 @@ cindices[20] = (4,5)
 
 # open logfile
 
-logfile = open("log.lammps",'r')
+with open("log.lammps",'r') as logfile:
-
     txt = logfile.read()
 
 # search for 21 elastic constants
@@ -56,7 +56,7 @@ s2 = 0
 for ival in range(nvals):
     s1 = txt.find(valstr,s2)
     if (s1 == -1):
-        print "Failed to find elastic constants in log file"
+        print("Failed to find elastic constants in log file")
         exit(1)
     s1 += 1
     s2 = txt.find("\n",s1)
@@ -67,11 +67,11 @@ for ival in range(nvals):
     c[i1,i2] = float(words[valpos])
     c[i2,i1] = c[i1,i2]
 
-print "C tensor [GPa]"
+print("C tensor [GPa]")
 for i in range(6):
     for j in range(6):
-        print "%10.8g " % c[i][j],
+        print("%10.8g " % c[i][j], end="")
-    print
+    print()
 
 # apply factor of 2 to columns of off-diagonal elements
 
@@ -87,9 +87,8 @@ for i in range(6):
     for j in range(3,6):
         s[i][j] *= 0.5
 
-print "S tensor [1/GPa]"
+print("S tensor [1/GPa]")
 for i in range(6):
     for j in range(6):
-        print "%10.8g " % s[i][j],
+        print("%10.8g " % s[i][j], end="")
-    print
+    print()
-        

python/.gitignore

@@ -1 +1,2 @@
 /build
+/*.egg-info

python/README

@@ -44,6 +44,7 @@ split.py            parallel example
 mc.py               Monte Carlo energy relaxation wrapper on LAMMPS
 gui.py              GUI go/stop/temperature-slider to control LAMMPS
 plot.py             real-time temperature plot with GnuPlot via Pizza.py
+matplotlib_plot.py  real-time temperature plot with Matplotlib via Pizza.py
 viz_tool.py         real-time viz via some viz package
 vizplotgui_tool.py  combination of viz.py and plot.py and gui.py
 
@@ -100,24 +101,24 @@ split.py in.simple       # can run in parallel (see below)
 
 gui.py in.gui 100
 plot.py in.plot 10 1000 thermo_temp
+matplotlib_plot.py in.plot 10 1000 thermo_temp
 viz_tool.py in.viz 100 5000
 vizplotgui_tool.py in.viz 100 thermo_temp
 
 To run LAMMPS in parallel from Python, so something like this:
 
-% mpirun -np 4 simple.py in.simple
+% mpirun -np P simple.py in.simple
-% mpirun -np 4 python split.py in.simple
+% mpirun -np P python split.py in.simple
 
 If you run simple.py as-is, this will invoke P instances of a
 one-processor run, where both Python and LAMMPS will run on single
 processors.  Each running job will read the same input file, and write
 to same log.lammps file, which isn't too useful.
 
-However, if you have either the Pypar or mpi4py packages installed in
+However, if you have the mpi4py Python package installed and uncomment mpi4py
-your Python, and uncomment the Pypar or mpi4py code in simple.py, then
+code in simple.py, then the above commands will invoke 1 instance of a
-the above commands will invoke 1 instance of a P-processor run.  Both
+P-processor run.  Both Python and LAMMPS will run on P processors.  The job will
-Python and LAMMPS will run on P processors.  The job will read the
+read the input file and write a single log.lammps file.
-input file and write a single log.lammps file.
 
 The split.py script can also be run in parallel.  It uses mpi4py
 version 2.0.0 (or later), which makes it possible to pass a

python/examples/.gitignore

@@ -0,0 +1 @@
+/tmp*

python/examples/gui.py

@@ -7,8 +7,7 @@
 #          in.lammps = LAMMPS input script
 #          Nfreq = query GUI every this many steps
 
-# IMPORTANT: this script cannot yet be run in parallel via Pypar,
+# IMPORTANT: this script cannot yet be run in parallel
-#            because I can't seem to do a MPI-style broadcast in Pypar
 
 from __future__ import print_function
 import sys,time
@@ -39,10 +38,6 @@ infile = sys.argv[1]
 nfreq = int(sys.argv[2])
 
 me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
 
 from lammps import lammps
 lmp = lammps()
@@ -110,7 +105,3 @@ while 1:
   if runflag: running = 1
   else: running = 0
   time.sleep(0.01)
-
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/matplotlib_plot.py

@@ -12,9 +12,6 @@
 
 from __future__ import print_function
 import sys
-sys.path.append("./pizza")
-import matplotlib
-matplotlib.use('tkagg')
 import matplotlib.pyplot as plt
 
 # parse command line
@@ -30,10 +27,10 @@ nsteps = int(sys.argv[3])
 compute = sys.argv[4]
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -79,14 +76,15 @@ while ntimestep < nsteps:
     ax = plt.gca()
     ax.relim()
     ax.autoscale_view(True, True, True)
-    fig.canvas.draw()
+    plt.pause(0.001)
+
 
 lmp.command("run 0 pre no post yes")
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()
 
+if me == 0:
   if sys.version_info[0] == 3:
       input("Press Enter to exit...")
   else:

python/examples/pizza/dump.py

@@ -275,7 +275,7 @@ class dump:
       print("no column assignments made")
     elif len(self.names):
       print("assigned columns:",self.names2str())
-    elif self.snaps[0].atoms == None:
+    elif self.snaps[0].atoms is None:
       print("no column assignments made")
     elif len(self.snaps[0].atoms[0]) == 5:
       self.map(1,"id",2,"type",3,"x",4,"y",5,"z")
@@ -969,12 +969,12 @@ class dump:
     xhi = yhi = zhi = None
     for snap in self.snaps:
       if not snap.tselect: continue
-      if xlo == None or snap.xlo < xlo: xlo = snap.xlo
+      if xlo is None or snap.xlo < xlo: xlo = snap.xlo
-      if xhi == None or snap.xhi > xhi: xhi = snap.xhi
+      if xhi is None or snap.xhi > xhi: xhi = snap.xhi
-      if ylo == None or snap.ylo < ylo: ylo = snap.ylo
+      if ylo is None or snap.ylo < ylo: ylo = snap.ylo
-      if yhi == None or snap.yhi > yhi: yhi = snap.yhi
+      if yhi is None or snap.yhi > yhi: yhi = snap.yhi
-      if zlo == None or snap.zlo < zlo: zlo = snap.zlo
+      if zlo is None or snap.zlo < zlo: zlo = snap.zlo
-      if zhi == None or snap.zhi > zhi: zhi = snap.zhi
+      if zhi is None or snap.zhi > zhi: zhi = snap.zhi
     return [xlo,ylo,zlo,xhi,yhi,zhi]
 
   # --------------------------------------------------------------------

python/examples/pizza/gl.py

@@ -851,7 +851,7 @@ class gl:
             ncolor = self.vizinfo.ntcolor
             for tri in self.tridraw:
               itype = int(tri[1])
-              if itype > ncolor: raise StandardError("tri type too big")
+              if itype > ncolor: raise Exception("tri type too big")
               red,green,blue = self.vizinfo.tcolor[itype]
               glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]);
               glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny);
@@ -909,7 +909,7 @@ class gl:
                    ymin >= ylo and ymax <= yhi and zmin >= zlo and zmax <= zhi:
               if bond[10] > bound: continue
               itype = int(bond[1])
-              if itype > ncolor: raise StandardError("bond type too big")
+              if itype > ncolor: raise Exception("bond type too big")
               red,green,blue = self.vizinfo.bcolor[itype]
               rad = self.vizinfo.brad[itype]
               glPushMatrix()
@@ -941,7 +941,7 @@ class gl:
                      ymin >= ylo and ymax <= yhi and \
                      zmin >= zlo and zmax <= zhi:
                 itype = int(tri[1])
-                if itype > ncolor: raise StandardError("tri type too big")
+                if itype > ncolor: raise Exception("tri type too big")
                 red,green,blue = self.vizinfo.tcolor[itype]
                 glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,
                              [red,green,blue,1.0]);

python/examples/pizza/gnu.py

@@ -87,12 +87,13 @@ g.curve(N,'r')                 set color of curve N
 
 # Imports and external programs
 
-import types, os
+import os
+import sys
 
 try: from DEFAULTS import PIZZA_GNUPLOT
-except: PIZZA_GNUPLOT = "gnuplot -p"
+except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
 try: from DEFAULTS import PIZZA_GNUTERM
-except: PIZZA_GNUTERM = "x11"
+except ImportError: PIZZA_GNUTERM = "x11"
 
 # Class definition
 
@@ -122,6 +123,9 @@ class gnu:
 
   def enter(self):
     while 1:
+      if sys.version_info[0] == 3:
+        command = input("gnuplot> ")
+      else:
         command = raw_input("gnuplot> ")
       if command == "quit" or command == "exit": return
       self.__call__(command)
@@ -136,7 +140,7 @@ class gnu:
       self.export(file,linear,vectors[0])
       self.figures[self.current-1].ncurves = 1
     else:
-      if len(vectors) % 2: raise StandardError("vectors must come in pairs")
+      if len(vectors) % 2: raise Exception("vectors must come in pairs")
       for i in range(0,len(vectors),2):
         file = self.file + ".%d.%d" % (self.current,i/2+1)
         self.export(file,vectors[i],vectors[i+1])
@@ -170,7 +174,7 @@ class gnu:
   def export(self,filename,*vectors):
     n = len(vectors[0])
     for vector in vectors:
-      if len(vector) != n: raise StandardError("vectors must be same length")
+      if len(vector) != n: raise Exception("vectors must be same length")
     f = open(filename,'w')
     nvec = len(vectors)
     for i in range(n):

python/examples/pizza/pdbfile.py

@@ -68,7 +68,7 @@ index,time,flag = p.iterator(1)
 
 # Imports and external programs
 
-import sys, types, glob, urllib
+import sys, glob, urllib
 PY3 = sys.version_info[0] == 3
 
 if PY3:
@@ -93,7 +93,7 @@ class pdbfile:
     elif len(args) == 2:
       filestr = args[0]
       self.data = args[1]
-    else: raise StandardError("invalid args for pdb()")
+    else: raise Exception("invalid args for pdb()")
 
     # flist = full list of all PDB input file names
     # append .pdb if needed
@@ -104,17 +104,17 @@ class pdbfile:
       for file in list:
         if '*' in file: flist += glob.glob(file)
         else: flist.append(file)
-      for i in xrange(len(flist)):
+      for i in range(len(flist)):
         if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
       if len(flist) == 0:
-        raise StandardError("no PDB file specified")
+        raise Exception("no PDB file specified")
       self.files = flist
     else: self.files = []
 
     if len(self.files) > 1 and self.data:
-      raise StandardError("cannot use multiple PDB files with data object")
+      raise Exception("cannot use multiple PDB files with data object")
     if len(self.files) == 0 and not self.data:
-      raise StandardError("no input PDB file(s)")
+      raise Exception("no input PDB file(s)")
 
     # grab PDB file from http://rcsb.org if not a local file
 

python/examples/pizza/vizinfo.py

@@ -79,7 +79,7 @@ class vizinfo:
     # if list of types has a 0, increment each type value
 
     if 0 in ids:
-      for i in xrange(len(ids)): ids[i] += 1
+      for i in range(len(ids)): ids[i] += 1
 
     # extend storage list if necessary
     # extend other arrays for same "which" so that gl::make_atom_calllist
@@ -109,7 +109,7 @@ class vizinfo:
     ntypes = len(ids)
     nrgbs = len(rgbs)
 
-    for i in xrange(ntypes):
+    for i in range(ntypes):
       id = ids[i]
 
       if rgbs[0] == "loop":
@@ -157,7 +157,7 @@ class vizinfo:
     # if list of types has a 0, increment each type value
 
     if 0 in ids:
-      for i in xrange(len(ids)): ids[i] += 1
+      for i in range(len(ids)): ids[i] += 1
 
     # extend storage list if necessary
     # extend other arrays for same "which" so that gl::make_atom_calllist
@@ -220,7 +220,7 @@ class vizinfo:
     # if list of types has a 0, increment each type value
 
     if 0 in ids:
-      for i in xrange(len(ids)): ids[i] += 1
+      for i in range(len(ids)): ids[i] += 1
 
     # extend storage list if necessary
     # extend other arrays for same "which" so that gl::make_atom_calllist
@@ -234,7 +234,7 @@ class vizinfo:
     # if list lengths match, set directly, else set types to 1st fill value
 
     if len(fills) == len(ids):
-      for i in xrange(len(ids)): self.tfill[ids[i]] = int(fills[i])
+      for i in range(len(ids)): self.tfill[ids[i]] = int(fills[i])
     else:
       for id in ids: self.tfill[id] = int(fills[0])
     

python/examples/pizza/vmd.py

@@ -45,17 +45,16 @@ v.debug([True|False])	       display generated VMD script commands?
 
 # Imports and external programs
 
-import types, os
+import os
-import numpy
 
 try: from DEFAULTS import PIZZA_VMDNAME
-except: PIZZA_VMDNAME = "vmd"
+except ImportError: PIZZA_VMDNAME = "vmd"
 try: from DEFAULTS import PIZZA_VMDDIR
-except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
+except ImportError: PIZZA_VMDDIR = "/usr/local/lib/vmd"
 try: from DEFAULTS import PIZZA_VMDDEV
-except: PIZZA_VMDDEV = "win"
+except ImportError: PIZZA_VMDDEV = "win"
 try: from DEFAULTS import PIZZA_VMDARCH
-except: PIZZA_VMDARCH = "LINUXAMD64"
+except ImportError: PIZZA_VMDARCH = "LINUXAMD64"
 
 # try these settings for a Mac
 #PIZZA_VMDNAME = "vmd"
@@ -64,7 +63,7 @@ except: PIZZA_VMDARCH = "LINUXAMD64"
 #PIZZA_VMDARCH = "MACOSXX86"
 
 try: import pexpect
-except: 
+except ImportError:
   print("pexpect from http://pypi.python.org/pypi/pexpect", \
       "is required for vmd tool")
   raise

python/examples/plot.py

@@ -28,10 +28,10 @@ nsteps = int(sys.argv[3])
 compute = sys.argv[4]
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -57,7 +57,7 @@ if me == 0:
   gn = gnu()
   gn.plot(xaxis,yaxis)
   gn.xrange(0,nsteps)
-  gn.title(compute,"Timestep","Temperature")
+  gn.title(compute.replace('_', ' '),"Timestep","Temperature")
 
 # run nfreq steps at a time w/out pre/post, query compute, refresh plot
 
@@ -71,6 +71,5 @@ while ntimestep < nsteps:
 
 lmp.command("run 0 pre no post yes")
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/simple.py

@@ -9,7 +9,7 @@
 
 # Parallel syntax: mpirun -np 4 simple.py in.lammps
 #                  in.lammps = LAMMPS input script
-# also need to uncomment either Pypar or mpi4py sections below
+# also need to uncomment mpi4py sections below
 
 from __future__ import print_function
 import sys
@@ -27,11 +27,6 @@ infile = sys.argv[1]
 
 me = 0
 
-# uncomment this if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
-
 # uncomment this if running in parallel via mpi4py
 #from mpi4py import MPI
 #me = MPI.COMM_WORLD.Get_rank()
@@ -133,8 +128,5 @@ lmp.reset_box([0,0,0],[10,10,8],0,0,0)
 boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()
 if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change)
 
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-
 # uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)

python/examples/viz_atomeye.py

@@ -28,10 +28,10 @@ nfreq = int(sys.argv[2])
 nsteps = int(sys.argv[3])
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -68,6 +68,5 @@ while ntimestep < nsteps:
 
 lmp.command("run 0 pre no post yes")
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/viz_gl.py

@@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
 nsteps = int(sys.argv[3])
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -83,6 +83,5 @@ while ntimestep < nsteps:
 
 lmp.command("run 0 pre no post yes")
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/viz_pymol.py

@@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
 nsteps = int(sys.argv[3])
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -78,6 +78,5 @@ while ntimestep < nsteps:
     
 lmp.command("run 0 pre no post yes")
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/viz_vmd.py

@@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
 nsteps = int(sys.argv[3])
 
 me = 0
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via mpi4py
-#import pypar
+#from mpi4py import MPI
-#me = pypar.rank()
+#me = MPI.COMM_WORLD.Get_rank()
-#nprocs = pypar.size()
+#nprocs = MPI.COMM_WORLD.Get_size()
 
 from lammps import lammps
 lmp = lammps()
@@ -87,6 +87,5 @@ if me == 0:
   #v.enter()
   #v.stop()
 
-# uncomment if running in parallel via Pypar
+# uncomment if running in parallel via mpi4py
 #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/vizplotgui_atomeye.py

@@ -9,9 +9,6 @@
 #          compute-ID = ID of compute that calculates temperature
 #                       (or any other scalar quantity)
 
-# IMPORTANT: this script cannot yet be run in parallel via Pypar,
-#            because I can't seem to do a MPI-style broadcast in Pypar
-
 from __future__ import print_function
 import sys,os,time
 sys.path.append("./pizza")
@@ -59,10 +56,6 @@ nfreq = int(sys.argv[2])
 compute = sys.argv[3]
 
 me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
 
 from lammps import lammps
 lmp = lammps()
@@ -163,7 +156,3 @@ while 1:
   time.sleep(0.01)
 
 lmp.command("run 0 pre no post yes")
-
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/vizplotgui_gl.py

@@ -9,9 +9,6 @@
 #          compute-ID = ID of compute that calculates temperature
 #                       (or any other scalar quantity)
 
-# IMPORTANT: this script cannot yet be run in parallel via Pypar,
-#            because I can't seem to do a MPI-style broadcast in Pypar
-
 from __future__ import print_function
 import sys,time
 sys.path.append("./pizza")
@@ -55,10 +52,6 @@ nfreq = int(sys.argv[2])
 compute = sys.argv[3]
 
 me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
 
 from lammps import lammps
 lmp = lammps()
@@ -176,7 +169,3 @@ while 1:
   time.sleep(0.01)
 
 lmp.command("run 0 pre no post yes")
-
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/vizplotgui_pymol.py

@@ -9,9 +9,6 @@
 #          compute-ID = ID of compute that calculates temperature
 #                       (or any other scalar quantity)
 
-# IMPORTANT: this script cannot yet be run in parallel via Pypar,
-#            because I can't seem to do a MPI-style broadcast in Pypar
-
 from __future__ import print_function
 import sys,time
 sys.path.append("./pizza")
@@ -57,10 +54,6 @@ nfreq = int(sys.argv[2])
 compute = sys.argv[3]
 
 me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
 
 from lammps import lammps
 lmp = lammps()
@@ -172,7 +165,3 @@ while 1:
   time.sleep(0.01)
 
 lmp.command("run 0 pre no post yes")
-
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/examples/vizplotgui_vmd.py

@@ -9,9 +9,6 @@
 #          compute-ID = ID of compute that calculates temperature
 #                       (or any other scalar quantity)
 
-# IMPORTANT: this script cannot yet be run in parallel via Pypar,
-#            because I can't seem to do a MPI-style broadcast in Pypar
-
 from __future__ import print_function
 import sys,time
 sys.path.append("./pizza")
@@ -56,10 +53,6 @@ nfreq = int(sys.argv[2])
 compute = sys.argv[3]
 
 me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
 
 from lammps import lammps
 lmp = lammps()
@@ -171,7 +164,3 @@ while 1:
   time.sleep(0.01)
 
 lmp.command("run 0 pre no post yes")
-
-# uncomment if running in parallel via Pypar
-#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
-#pypar.finalize()

python/lammps/__init__.py

@@ -25,18 +25,18 @@ def get_version_number():
 
     vstring = None
     if version_info.major == 3 and version_info.minor >= 8:
-        from importlib.metadata import version
+        from importlib.metadata import version, PackageNotFoundError
         try:
             vstring = version('lammps')
-        except:                         # lgtm [py/catch-base-exception]
+        except PackageNotFoundError:
             # nothing to do, ignore
             pass
 
     else:
-        from pkg_resources import get_distribution
+        from pkg_resources import get_distribution, DistributionNotFound
         try:
             vstring = get_distribution('lammps').version
-        except:                         # lgtm [py/catch-base-exception]
+        except DistributionNotFound:
             # nothing to do, ignore
             pass
 

python/lammps/constants.py

@@ -11,8 +11,6 @@
 #   See the README file in the top-level LAMMPS directory.
 # -------------------------------------------------------------------------
 
-from ctypes import c_int, c_int32, c_int64
-
 # various symbolic constants to be used
 # in certain calls to select data formats
 LAMMPS_AUTODETECT = None
@@ -42,6 +40,7 @@ LMP_VAR_ATOM  = 1
 # -------------------------------------------------------------------------
 
 def get_ctypes_int(size):
+  from ctypes import c_int, c_int32, c_int64
   if size == 4:
     return c_int32
   elif size == 8:

python/lammps/core.py

@@ -100,7 +100,7 @@ class lammps(object):
 
     try:
       if ptr: self.lib = CDLL("",RTLD_GLOBAL)
-    except:                             # lgtm [py/catch-base-exception]
+    except OSError:
       self.lib = None
 
     # load liblammps.so unless name is given
@@ -307,13 +307,12 @@ class lammps(object):
         from mpi4py import __version__ as mpi4py_version
         # tested to work with mpi4py versions 2 and 3
         self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
-      except:                           # lgtm [py/catch-base-exception]
+      except ImportError:
         # ignore failing import
         pass
 
     # if no ptr provided, create an instance of LAMMPS
-    #   don't know how to pass an MPI communicator from PyPar
+    #   we can pass an MPI communicator from mpi4py v2.0.0 and later
-    #   but we can pass an MPI communicator from mpi4py v2.0.0 and later
     #   no_mpi call lets LAMMPS use MPI_COMM_WORLD
     #   cargs = array of C strings from args
     # if ptr, then are embedding Python in LAMMPS input script
@@ -1134,10 +1133,10 @@ class lammps(object):
     with ExceptionCheck(self):
       if dtype == 0:
         data = ((count*natoms)*c_int)()
-        self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
+        self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
       elif dtype == 1:
         data = ((count*natoms)*c_double)()
-        self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
+        self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
       else:
         return None
     return data
@@ -1150,10 +1149,10 @@ class lammps(object):
     with ExceptionCheck(self):
       if dtype == 0:
         data = ((count*natoms)*c_int)()
-        self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
+        self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
       elif dtype == 1:
         data = ((count*natoms)*c_double)()
-        self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
+        self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
       else:
           return None
     return data

python/setup.py

@@ -8,8 +8,14 @@ LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
 LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
 LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
 
+if not os.path.exists(LAMMPS_SOURCE_DIR):
+    # allows installing and building wheel from current directory
+    LAMMPS_DIR = os.path.realpath(os.path.join(os.environ['PWD'], '..'))
+    LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
+
 def get_lammps_version():
-    with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
+    version_h_file = os.path.join(LAMMPS_SOURCE_DIR, 'version.h')
+    with open(version_h_file, 'r') as f:
         line = f.readline()
         start_pos = line.find('"')+1
         end_pos = line.find('"', start_pos)

tools/python/pizza/gnu.py

@@ -6,6 +6,9 @@
 # certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
+# for python3 compatibility
+from __future__ import print_function
+
 # gnu tool
 
 oneline = "Create plots via GnuPlot plotting program"
@@ -84,12 +87,13 @@ g.curve(N,'r')                 set color of curve N
 
 # Imports and external programs
 
-import types, os
+import os
+import sys
 
 try: from DEFAULTS import PIZZA_GNUPLOT
-except: PIZZA_GNUPLOT = "gnuplot"
+except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
 try: from DEFAULTS import PIZZA_GNUTERM
-except: PIZZA_GNUTERM = "x11"
+except ImportError: PIZZA_GNUTERM = "x11"
 
 # Class definition
 
@@ -119,6 +123,9 @@ class gnu:
 
   def enter(self):
     while 1:
+      if sys.version_info[0] == 3:
+        command = input("gnuplot> ")
+      else:
         command = raw_input("gnuplot> ")
       if command == "quit" or command == "exit": return
       self.__call__(command)
@@ -133,7 +140,7 @@ class gnu:
       self.export(file,linear,vectors[0])
       self.figures[self.current-1].ncurves = 1
     else:
-      if len(vectors) % 2: raise StandardError,"vectors must come in pairs"
+      if len(vectors) % 2: raise Exception("vectors must come in pairs")
       for i in range(0,len(vectors),2):
         file = self.file + ".%d.%d" % (self.current,i/2+1)
         self.export(file,vectors[i],vectors[i+1])
@@ -167,13 +174,13 @@ class gnu:
   def export(self,filename,*vectors):
     n = len(vectors[0])
     for vector in vectors:
-      if len(vector) != n: raise StandardError,"vectors must be same length"
+      if len(vector) != n: raise Exception("vectors must be same length")
     f = open(filename,'w')
     nvec = len(vectors)
-    for i in xrange(n):
+    for i in range(n):
-      for j in xrange(nvec):
+      for j in range(nvec):
-        print >>f,vectors[j][i],
+        print(str(vectors[j][i])+" ",file=f,end='')
-      print >>f
+      print ("",file=f)
     f.close()
 
   # --------------------------------------------------------------------
@@ -350,7 +357,7 @@ class gnu:
 
     self.__call__("set key off")
     cmd = 'plot '
-    for i in range(fig.ncurves):
+    for i in range(int(fig.ncurves)):
       file = self.file + ".%d.%d" % (self.current,i+1)
       if len(fig.colors) > i and fig.colors[i]:
         cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]

tools/python/pizza/pdbfile.py

@@ -6,6 +6,9 @@
 # certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
+# for python3 compatibility
+from __future__ import print_function
+
 # pdb tool
 
 oneline = "Read, write PDB files in combo with LAMMPS snapshots"
@@ -51,6 +54,7 @@ index,time,flag = p.iterator(1)
 
 # History
 #   8/05, Steve Plimpton (SNL): original version
+#   3/17, Richard Berger (Temple U): improve Python 3 compatibility
 
 # ToDo list
 #   for generic PDB file (no template) from a LJ unit system,
@@ -64,7 +68,13 @@ index,time,flag = p.iterator(1)
 
 # Imports and external programs
 
-import sys, types, glob, urllib
+import sys, glob, urllib
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+    string_types = str,
+else:
+    string_types = basestring
 
 # Class definition
 
@@ -74,7 +84,7 @@ class pdbfile:
 
   def __init__(self,*args):
     if len(args) == 1:
-      if type(args[0]) is types.StringType:
+      if type(args[0]) is string_types:
         filestr = args[0]
         self.data = None
       else:
@@ -83,7 +93,7 @@ class pdbfile:
     elif len(args) == 2:
       filestr = args[0]
       self.data = args[1]
-    else: raise StandardError, "invalid args for pdb()"
+    else: raise Exception("invalid args for pdb()")
 
     # flist = full list of all PDB input file names
     # append .pdb if needed
@@ -94,17 +104,17 @@ class pdbfile:
       for file in list:
         if '*' in file: flist += glob.glob(file)
         else: flist.append(file)
-      for i in xrange(len(flist)):
+      for i in range(len(flist)):
         if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
       if len(flist) == 0:
-        raise StandardError,"no PDB file specified"
+        raise Exception("no PDB file specified")
       self.files = flist
     else: self.files = []
 
     if len(self.files) > 1 and self.data:
-      raise StandardError, "cannot use multiple PDB files with data object"
+      raise Exception("cannot use multiple PDB files with data object")
     if len(self.files) == 0 and not self.data:
-      raise StandardError, "no input PDB file(s)"
+      raise Exception("no input PDB file(s)")
 
     # grab PDB file from http://rcsb.org if not a local file
 
@@ -112,7 +122,7 @@ class pdbfile:
       try:
         open(self.files[0],'r').close()
       except:
-        print "downloading %s from http://rcsb.org" % self.files[0]
+        print("downloading %s from http://rcsb.org" % self.files[0])
         fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
         urllib.urlretrieve(fetchstr,self.files[0])
 
@@ -142,20 +152,20 @@ class pdbfile:
         which,time,flag = self.data.iterator(flag)
         if flag == -1: break
         self.convert(f,which)
-        print >>f,"END"
+        print("END",file=f)
-        print time,
+        print(time,end='')
         sys.stdout.flush()
         n += 1
 
     else:
       for file in self.files:
         f.write(open(file,'r').read())
-        print >>f,"END"
+        print("END",file=f)
-        print file,
+        print(file,end='')
         sys.stdout.flush()
 
     f.close()
-    print "\nwrote %d datasets to %s in PDB format" % (n,file)
+    print("\nwrote %d datasets to %s in PDB format" % (n,file))
 
   # --------------------------------------------------------------------
   # write series of numbered PDB files
@@ -190,7 +200,7 @@ class pdbfile:
         self.convert(f,which)
         f.close()
 
-        print time,
+        print(time,end='')
         sys.stdout.flush()
         n += 1
 
@@ -210,12 +220,12 @@ class pdbfile:
         f = open(file,'w')
         f.write(open(infile,'r').read())
         f.close()
-        print file,
+        print(file,end='')
         sys.stdout.flush()
 
         n += 1
 
-    print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
+    print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
 
   # --------------------------------------------------------------------
   # write a single PDB file
@@ -280,10 +290,10 @@ class pdbfile:
         if self.atomlines.has_key(id):
           (begin,end) = self.atomlines[id]
           line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
-          print >>f,line,
+          print(line,file=f,end='')
     else:
       for atom in atoms:
         begin = "ATOM %6d %2d   R00     1    " % (atom[0],atom[1])
         middle = "%8.3f%8.3f%8.3f" %  (atom[2],atom[3],atom[4])
         end = "  1.00  0.00    NONE"
-        print >>f,begin+middle+end
+        print(begin+middle+end,file=f)