rename 'list' variables

python 2 vs 3 imports

examples/files/dump.kinase

@@ -6,7 +6,7 @@ ITEM: BOX BOUNDS
 -6.2035 6.2035
 -6.2035 6.2035
 -6.2035 6.2035
-ITEM: ATOMS
+ITEM: ATOMS id type x y z
 1965739326 1 -2.73852 3.76042 0.0137829
 1638062651 1 -4.08446 0.411239 0.994664
 574343881 1 -2.25466 -3.0259 -0.036883

examples/files/dump.micelle

@@ -6,7 +6,7 @@ ITEM: BOX BOUNDS
 0 35.8569
 0 35.8569
 -0.1 0.1
-ITEM: ATOMS
+ITEM: ATOMS id type xs ys zs
 1 2 0.972698 0.992397 0.5
 2 1 0.0517232 0.999069 0.5
 3 1 0.0504894 0.0385782 0.5

examples/files/dump.peptide

@@ -6,7 +6,7 @@
    36.8401937129895        64.2115601793071     
    41.0136911525442        68.3850576188589     
    29.7680952261698        57.1394616924871     
- ITEM: ATOMS
+ ITEM: ATOMS id type xs ys zs ix iy iz
     31  3  0.22450  0.39503  0.37295    0    0    0
    306 14  0.29326  0.17604  0.15395    0    0    0
     16  8  0.31495  0.27307  0.07008    0    0    0

examples/files/dump.peptide.1

@@ -6,7 +6,7 @@ ITEM: BOX BOUNDS
 0 27.9398
 0 27.9398
 0 27.9398
-ITEM: ATOMS
+ITEM: ATOMS id type xs ys zs ix iy iz
 1 1 0.410912 0.570945 0.36491 0 0 0
 2 2 0.376227 0.6013 0.339084 0 0 0
 3 3 0.397383 0.536983 0.387988 0 0 0

examples/files/dump.peptide.2

@@ -6,7 +6,7 @@ ITEM: BOX BOUNDS
 0.482127 27.3191
 0.477796 27.3148
 0.47406 27.3111
-ITEM: ATOMS
+ITEM: ATOMS id type xs ys zs ix iy iz
 1 1 0.404224 0.524373 0.362448 0 0 0
 2 2 0.364265 0.561026 0.358768 0 0 0
 3 3 0.394989 0.481736 0.350359 0 0 0

examples/group_energy.py

@@ -5,6 +5,8 @@
 
 # return distance sq between 2 atoms with PBC
 
+from __future__ import absolute_import
+
 def distance(box,x1,y1,z1,x2,y2,z2):
 
   delx = x2 - x1
@@ -37,12 +39,12 @@ def distance(box,x1,y1,z1,x2,y2,z2):
 # main script
 
 if len(argv) < 3:
-  raise StandardError,"group_energy.py data.file dump.file1 dump.file2 ..."
+  raise Exception("group_energy.py data.file dump.file1 dump.file2 ...")
 
-dt = data(argv[1])				# data file
+dt = data(argv[1])                              # data file
 q = dt.get("Atoms",4)
 
-files = ' '.join(argv[2:])		        # dump files
+files = ' '.join(argv[2:])                      # dump files
 d = dump(files,0)
 d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
 
@@ -75,32 +77,32 @@ while 1:
   d.aselect.test("$id >= 1 and $id <= 7243 or $id >= 7274 and $id <= 14283",
                  time)
   id2,type2,x2,y2,z2 = d.vecs(time,"id","type","x","y","z")
-  id1 = map(int,id1)
+  id1 = list(map(int,id1))
-  id2 = map(int,id2)
+  id2 = list(map(int,id2))
-  type1 = map(int,type1)
+  type1 = list(map(int,type1))
-  type2 = map(int,type2)
+  type2 = list(map(int,type2))
   n1 = len(type1)
   n2 = len(type2)
-  for i in xrange(n1): 
+  for i in range(n1):
     id1[i] -= 1
     type1[i] -= 1
-  for i in xrange(n2): 
+  for i in range(n2):
     id2[i] -= 1
     type2[i] -= 1
 
   e_coul_sum = 0.0
   e_vdwl_sum = 0.0
-  for i in xrange(n1):
+  for i in range(n1):
     typei = type1[i]
     qi = q[id1[i]]
-    for j in xrange(n2):
+    for j in range(n2):
       rsq = distance(box,x1[i],y1[i],z1[i],x2[j],y2[j],z2[j])
       if rsq < maxcut_sq:
         eng_coul,eng_vdwl = p.single(rsq,typei,type2[j],qi,q[id2[j]])
         e_coul_sum += eng_coul
         e_vdwl_sum += eng_vdwl
-  print "eng_coul = %g at timestep %d" % (e_coul_sum,time)
+  print("eng_coul = %g at timestep %d" % (e_coul_sum,time))
-  print "eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time)
+  print("eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time))
 
   d.tselect.none()
   d.tselect.one(time)

examples/movie_flow.py

@@ -1,5 +1,7 @@
 # movie of flow around obstacle
 
+from __future__ import absolute_import
+
 d = dump("dump.flow")
 d.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"vx",7,"vy")
 d.set("$ke = sqrt($vx*$vx + $vy*$vy)")
@@ -7,8 +9,8 @@ d.spread("vx",100,"color")
 d.atype = "color"
 
 r = raster(d)
-r.acol(range(100),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
+r.acol(list(range(100)),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
-r.arad(range(100),0.5)
+r.arad(list(range(100)),0.5)
 r.rotate(0,-90)
 r.zoom(1.5)
 r.file = "flow"

examples/movie_melt.py

@@ -1,6 +1,6 @@
 # movie of melting LJ solid
 
-a = dump("dump.melt")
+a = dump("files/dump.melt")
 a.tselect.test("$t == 0")
 a.scale()
 a.set("$ix = int($x * 4)")

examples/movie_micelle.py

@@ -1,10 +1,12 @@
 # movie of self-assembling micelles
 
-d = dump("dump.micelle")
+from __future__ import absolute_import
+
+d = dump("files/dump.micelle")
 
 s = svg(d)
 s.acol([1,2,3,4],["blue","red","cyan","yellow"])
-s.arad(range(4),0.5)
+s.arad(list(range(4)),0.5)
 s.zoom(1.5)
 
 s.file = "micelle"

examples/movie_peptide.py

@@ -1,8 +1,8 @@
 # movie of solvated peptide data
 
-d = dump("dump.peptide")
+d = dump("files/dump.peptide")
 d.unwrap()
-p = pdb("peptide",d)
+p = pdbfile("files/peptide",d)
-r.file = "peptide"
+
 r = rasmol(p)
 r.all()

examples/movie_tri.py

@@ -1,6 +1,6 @@
 # movie of triangular particle data
 
-d = dump("dump.tri")
+d = dump("files/dump.tri")
 d.set("$center = ((int($id)-1)/36+1)*36")
 d.owrap("center")
 

examples/test_animate.py

@@ -11,4 +11,4 @@ a.next()
 a.previous()
 a.frame(1)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_bdump.py

@@ -9,4 +9,4 @@ dm.extra(b)
 g = gl(dm)
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_cdata.py

@@ -31,4 +31,4 @@ c.select("A","B","C","linebox","organelle","nuchalf")
 g = gl(c)
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_cfg.py

@@ -9,4 +9,4 @@ x.one()
 x.many()
 x.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_chain.py

@@ -14,4 +14,4 @@ c.build(10,25)
 
 c.write("tmp.data.chain")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_clog.py

@@ -4,13 +4,13 @@
 
 c = log("files/log.ccell")
 
-print "# of vectors =",c.nvec
+print("# of vectors =",c.nvec)
-print "length of vectors =",c.nlen
+print("length of vectors =",c.nlen)
-print "names of vectors =",c.names
+print("names of vectors =",c.names)
 
 time,a,b = c.get("Step","prey","predator")
-print a,b
+print(a,b)
 c.write("tmp.clog")
 c.write("tmp.clog.two","Step","prey")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_data.py

@@ -1,18 +1,20 @@
 # simple test of data tool
-# requires files/data.micelle
+# requires files/data.micelle and dump.micelle
 # creates tmp.data
 
+from __future__ import absolute_import
+
 d = data("files/data.micelle")
 d.map(1,"id",3,"type",4,"x",5,"y",6,"z")
 coeffs = d.get("Masses")
-print "Masses",coeffs
+print("Masses",coeffs)
 x = d.get("Atoms",4)
-print "X of 1st atom",x[0]
+print("X of 1st atom",x[0])
 
 d.title = "New LAMMPS data file"
 
 natoms = d.headers["atoms"]
-vec = range(1,natoms+1)
+vec = list(range(1,natoms+1))
 vec.reverse()
 d.replace("Atoms",1,vec)
 
@@ -27,4 +29,4 @@ while 1:
 
 d.write("tmp.data")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_dump.py

@@ -27,12 +27,12 @@ d.set("$xyz = $x + $y + $z")
 d.spread("x",100,"color")
 d.clone(0,"color")
 
-print "Time",d.time()
+print("Time",d.time())
 color = d.atom(1,"color")
-print "Color of atom 1",color
+print("Color of atom 1",color)
 d.aselect.test("$id <= 10")
 color = d.vecs(1000,"color")
-print "Color of 1st 10 atoms in step 1000",color
+print("Color of 1st 10 atoms in step 1000",color)
 
 d.atype = "color"
 
@@ -42,13 +42,13 @@ while 1:
   if flag == -1: break
   time,box,atoms,bonds,tris,lines = d.viz(index)
   colors = [atom[1] for atom in atoms]
-  print time,colors
+  print(time,colors)
 
 d = dump("files/dump.peptide.*",0)
 while 1:
   time = d.next()
   if time < 0: break
 
-print "Incrementally read snaps =",d.nsnaps
+print("Incrementally read snaps =",d.nsnaps)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_ensight.py

@@ -1,4 +1,4 @@
-# simple test of xyz tool
+# simple test of ensight tool
 # requires files/dump.micelle.*
 # creates tmp*.case, etc
 
@@ -8,4 +8,4 @@ e.one()
 e.many()
 e.single(0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_gl.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 g = gl(d)
 
@@ -17,7 +19,7 @@ g.all()
 from vizinfo import colors
 
 g.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-g.arad(range(9),0.3)
+g.arad(list(range(9)),0.3)
 #g.label(0.2,0.4,'h',15,"red","test label #1")
 #g.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
@@ -25,4 +27,4 @@ g.show(0)
 g.pan(60,130,1,60,30,0.5)
 g.all(0,10,0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_gnu.py

@@ -1,17 +1,19 @@
 # simple test of gnu tool
 # creates tmp.eps
 
+from __future__ import absolute_import
+
 g = gnu()
 
 g("plot sin(x) with lines")
 
-a = range(10)
+a = list(range(10))
 b = [3,6,2,5,7,3,6,5,3,1]
 
 g.plot(a)
 g.plot(a,b)
 g.plot(a,b,b,a)
-g.mplot(0,10,2,"tmp",a,b)
+g.mplot(2,10,2,"tmp",a,b)
 
 g.export("tmp.gnu",a,b)
 
@@ -30,4 +32,4 @@ g.ylog()
 
 g.save("tmp")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_histo.py

@@ -10,4 +10,4 @@ g.ytitle("Particle Count")
 g.title("Histogram of Particle Density")
 g.plot(x,y)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_image.py

@@ -4,6 +4,6 @@
 i = image("files/bucky*.png")
 i.convert("files/bucky*.png","tmp*.gif")
 i.montage("","files/bucky*.png","tmp*.gif","tmpnew*.png")
-i.view("")
+i.view("*.png")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_ldump.py

@@ -12,4 +12,4 @@ g.lrad(1,5)
 g.lcol(1,"green")
 v = vcr(g)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_log.py

@@ -4,13 +4,13 @@
 
 lg = log("files/log.obstacle")
 
-print "# of vectors =",lg.nvec
+print("# of vectors =",lg.nvec)
-print "length of vectors =",lg.nlen
+print("length of vectors =",lg.nlen)
-print "names of vectors =",lg.names
+print("names of vectors =",lg.names)
 
 time,temp,press = lg.get("Step","Temp","Press")
-print temp,press
+print(temp,press)
 lg.write("tmp.log")
 lg.write("tmp.log.two","Step","E_pair")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_matlab.py

@@ -1,9 +1,11 @@
 # simple test of matlab tool
 # creates tmp.eps
 
+from __future__ import absolute_import
+
 m = matlab()
 
-a = range(10)
+a = list(range(10))
 b = [3,6,2,5,7,3,6,5,3,1]
 
 m.plot(a)
@@ -30,4 +32,4 @@ m.ylog()
 
 m.save("tmp")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_mdump.py

@@ -12,7 +12,7 @@ m.tselect.all()
 m.tselect.test("$t >= 100 and $t <= 200")
 m.delete()
 
-print "Time",m.time()
+print("Time",m.time())
 
 m.map(2,"spin")
 m.etype = "spin"
@@ -23,13 +23,13 @@ while 1:
   if flag == -1: break
   time,box,atoms,bonds,tris,lines = m.viz(index)
   colors = [tri[1] for tri in tris]
-  print time,colors
+  print(time,colors)
 
 m = dump("files/mesh.grain",0)
 while 1:
   time = m.next()
   if time < 0: break
 
-print "Incrementally read snaps =",m.nsnaps
+print("Incrementally read snaps =",m.nsnaps)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_pair.py

@@ -6,6 +6,6 @@ d = data("files/data.rhodo")
 p.coeff(d)
 p.init(8.0,10.0)
 ev,ec = p.single(5.0,1,2,0.5,-0.5)
-print "Energies",ev,ec
+print("Energies",ev,ec)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_patch.py

@@ -7,4 +7,4 @@ p.build(100,"hex2",1,2,3)
 p.build(50,"tri5",4,5)
 p.write("tmp.data.patch")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_pdbfile.py

@@ -15,6 +15,6 @@ while 1:
   p.single(time,"tmp.single")
   n += 1
 
-print "Incrementally processed %d PDB files" % n
+print("Incrementally processed %d PDB files" % n)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_plotview.py

@@ -15,4 +15,4 @@ p.no(2)
 p.file("tmp.plotview")
 p.save()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_rasmol.py

@@ -8,14 +8,14 @@ p = pdbfile("files/peptide",d)
 r = rasmol(p)
 r.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.all()
 
 # change RasMol settings, run all() with those settings
 
-print "change RasMol settings as desired, then type 'quit' ..."
+print("change RasMol settings as desired, then type 'quit' ...")
 r.run(0)
 r.all("tmp.rasmol")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_raster.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 r = raster(d)
 
@@ -10,7 +12,7 @@ r.rotate(60,130)
 r.box(1)
 r.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.all()
 a1 = animate("tmp0*png")
@@ -18,14 +20,14 @@ a1 = animate("tmp0*png")
 from vizinfo import colors
 
 r.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-r.arad(range(9),0.3)
+r.arad(list(range(9)),0.3)
 r.label(0.2,0.4,'h',15,"red","test label #1")
 r.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 r.show(0)
 r.pan(60,130,1,60,30,0.5)
 r.all(0,10,0)
 a2 = animate("tmp0*png")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_svg.py

@@ -2,6 +2,8 @@
 # requires files/dump.kinase
 # creates tmp*.png
 
+from __future__ import absolute_import
+
 d = dump("files/dump.kinase")
 s = svg(d)
 
@@ -10,20 +12,20 @@ s.rotate(60,130)
 s.box(1)
 s.file = "tmp"
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 s.show(0)
 s.all()
 
 from vizinfo import colors
 
 s.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
-s.arad(range(9),0.3)
+s.arad(list(range(9)),0.3)
 s.label(0.2,0.4,'h',15,"red","test label #1")
 s.label(-0.2,-0.4,'h',15,"yellow","test label #2")
 
-print "kill image window when ready to contine ..."
+print("kill image window when ready to contine ...")
 s.show(0)
 s.pan(60,130,1,60,30,0.5)
 s.all(0,10,0)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vcr.py

@@ -1,5 +1,4 @@
 # simple test of vcr tool
-# requires files/bucky*png files
 
 d = dump("files/dump.micelle")
 dt = data("files/data.micelle")
@@ -14,4 +13,4 @@ v.clipxlo(0.2)
 v.clipxhi(0.5)
 v.play()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vec.py

@@ -4,13 +4,13 @@
 
 v = vec("files/vec.txt")
 
-print "# of vectors =",v.nvec
+print("# of vectors =",v.nvec)
-print "length of vectors =",v.nlen
+print("length of vectors =",v.nlen)
-print "names of vectors =",v.names
+print("names of vectors =",v.names)
 
 time,temp,press = v.get(1,"col2",6)
-print temp,press
+print(temp,press)
 v.write("tmp.vec")
 v.write("tmp.vec.two","col1",3)
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vmd.py

@@ -8,4 +8,4 @@ v.rep('VDW')
 v.new('files/peptide.pdb','pdb')
 v.flush()
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_vtk.py

@@ -8,4 +8,4 @@ v.one()
 v.many()
 v.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

examples/test_xyz.py

@@ -8,4 +8,4 @@ x.one()
 x.many()
 x.single(0,"tmp.single")
 
-print "all done ... type CTRL-D to exit Pizza.py"
+print("all done ... type CTRL-D to exit Pizza.py")

scripts/angle_distribute.py

@@ -17,13 +17,12 @@
 import sys
 from dump import dump
 from math import sqrt,acos,atan
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 7:
-  raise StandardError, \
+  raise Exception("Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ...")
-  "Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ..."
 
 dt = data(argv[1])
 nbins = int(argv[2])
@@ -40,18 +39,18 @@ atype = nangles * [0]
 iatom = nangles * [0]
 jatom = nangles * [0]
 katom = nangles * [0]
-for i in xrange(nangles):
+for i in range(nangles):
   atype[i] = int(angle[i][1] - 1)
   iatom[i] = int(angle[i][2] - 1)
   jatom[i] = int(angle[i][3] - 1)
   katom[i] = int(angle[i][4] - 1)
 
 ntypes = 0
-for i in xrange(nangles): ntypes = max(angle[i][1],ntypes)
+for i in range(nangles): ntypes = max(angle[i][1],ntypes)
 ntypes = int(ntypes)
 ncount = ntypes * [0]
 bin = nbins * [0]
-for i in xrange(nbins): 
+for i in range(nbins):
   bin[i] = ntypes * [0]
 
 # read snapshots one-at-a-time
@@ -76,7 +75,7 @@ while 1:
   d.sort()
   x,y,z = d.vecs(time,"x","y","z")
 
-  for i in xrange(nangles):
+  for i in range(nangles):
 
     delx1 = x[iatom[i]] - x[jatom[i]]
     dely1 = y[iatom[i]] - y[jatom[i]]
@@ -135,22 +134,22 @@ while 1:
       bin[ibin][atype[i]] += nbins
       ncount[atype[i]] += 1
     else:
-      print "Warning: angle outside specified range"
+      print("Warning: angle outside specified range")
-      print "angle type:", atype[i]+1
+      print("angle type:", atype[i]+1)
-      print "angle number:", i
+      print("angle number:", i)
-  print time,    
+  print(time, end=' ')
 
-print
+print()
-print "Printing normalized angle distributions to",outfile
+print("Printing normalized angle distributions to",outfile)
 
 fp = open(outfile,"w")
 theta_range = theta_max - theta_min
-for i in xrange(nbins):
+for i in range(nbins):
-  print >>fp, theta_min + theta_range*float(i)/float(nbins), 
+  print(theta_min + theta_range*float(i)/float(nbins), end=' ', file=fp)
-  for j in xrange(ntypes):
+  for j in range(ntypes):
     if (ncount[j] > 0):
-      print >>fp, float(bin[i][j])/float(ncount[j])/theta_range,
+      print(float(bin[i][j])/float(ncount[j])/theta_range, end=' ', file=fp)
     else:
-      print >>fp, 0.0,    
+      print(0.0, end=' ', file=fp)
-  print >>fp 
+  print(file=fp)
 fp.close()

scripts/block.py

@@ -13,12 +13,12 @@
 
 import sys
 from log import log
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 4:
-  raise StandardError, "Syntax: block.py nblocks nskip log.1 log.2 ..."
+  raise Exception("Syntax: block.py nblocks nskip log.1 log.2 ...")
 
 nblocks = int(argv[1])
 nskip = int(argv[2])
@@ -35,8 +35,8 @@ if "Volume" in l.names:
   volume = l.get("Volume")
 else: vflag = 0
 
-print "Computing %g block averages" % nblocks
+print("Computing %g block averages" % nblocks)
-print "Skipping first %g samples" % nskip
+print("Skipping first %g samples" % nskip)
 
 n = len(step)
 n_per_block = (n-nskip)/nblocks
@@ -48,11 +48,11 @@ e_total_ave = []
 pressure_ave = []
 volume_ave = []
 
-print
+print()
-print " Block    Samples Temperature      E_bond      E_pair",  \
+print(" Block    Samples Temperature      E_bond      E_pair",  \
-  "    E_total    Pressure      Volume"
+  "    E_total    Pressure      Volume")
 
-for i in xrange(nblocks):
+for i in range(nblocks):
   temperature_sum = 0
   e_bond_sum = 0
   e_pair_sum = 0
@@ -60,7 +60,7 @@ for i in xrange(nblocks):
   pressure_sum = 0
   volume_sum = 0
   samples = 0
-  for j in xrange(n_per_block): 
+  for j in range(n_per_block):
     temperature_sum += temperature[k]
     e_bond_sum += e_bond[k]
     e_pair_sum += e_pair[k]
@@ -75,9 +75,9 @@ for i in xrange(nblocks):
   e_total_ave.append(e_total_sum/samples)
   pressure_ave.append(pressure_sum/samples)
   volume_ave.append(volume_sum/samples)
-  print " %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" %  \
+  print(" %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" %  \
     (i+1, samples, temperature_ave[i], e_bond_ave[i], e_pair_ave[i], \
-    e_total_ave[i], pressure_ave[i], volume_ave[i])
+    e_total_ave[i], pressure_ave[i], volume_ave[i]))
 
 grand_ave_temperature = 0.0
 grand_ave_e_bond = 0.0
@@ -91,7 +91,7 @@ stdev_e_pair = 0.0
 stdev_e_total = 0.0
 stdev_pressure = 0.0
 stdev_volume = 0.0
-for i in xrange(nblocks):
+for i in range(nblocks):
   grand_ave_temperature += temperature_ave[i]
   grand_ave_e_bond += e_bond_ave[i]
   grand_ave_e_pair += e_pair_ave[i]
@@ -104,7 +104,7 @@ grand_ave_e_pair /= nblocks
 grand_ave_e_total /= nblocks
 grand_ave_pressure /= nblocks
 grand_ave_volume /= nblocks
-for i in xrange(nblocks):
+for i in range(nblocks):
   stdev_temperature += (temperature_ave[i] - grand_ave_temperature)*  \
                        (temperature_ave[i] - grand_ave_temperature)
   stdev_e_bond += (e_bond_ave[i] - grand_ave_e_bond)*  \
@@ -125,13 +125,13 @@ stdev_e_total = sqrt(stdev_e_total/(nblocks-1))
 stdev_pressure = sqrt(stdev_pressure/(nblocks-1))
 stdev_volume = sqrt(stdev_volume/(nblocks-1))
 
-print " ====================================================",  \
+print(" ====================================================",  \
-  "==================================="
+  "===================================")
 
-print " Ave.             %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
+print(" Ave.             %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
     (grand_ave_temperature, grand_ave_e_bond, grand_ave_e_pair, \
-    grand_ave_e_total, grand_ave_pressure, grand_ave_volume)
+    grand_ave_e_total, grand_ave_pressure, grand_ave_volume))
 
-print " Stdev            %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
+print(" Stdev            %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
     (stdev_temperature, stdev_e_bond, stdev_e_pair, \
-    stdev_e_total, stdev_pressure, stdev_volume)
+    stdev_e_total, stdev_pressure, stdev_volume))

scripts/bond_distribute.py

@@ -17,13 +17,12 @@
 import sys
 from dump import dump
 from math import sqrt
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 7:
-  raise StandardError, \
+  raise Exception("Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ...")
-   "Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ..."
 
 dt = data(argv[1])
 nbins = int(argv[2])
@@ -39,17 +38,17 @@ nbonds = len(bond)
 btype = nbonds * [0]
 iatom = nbonds * [0]
 jatom = nbonds * [0]
-for i in xrange(nbonds):
+for i in range(nbonds):
   btype[i] = int(bond[i][1] - 1)
   iatom[i] = int(bond[i][2] - 1)
   jatom[i] = int(bond[i][3] - 1)
 
 ntypes = 0
-for i in xrange(nbonds): ntypes = max(bond[i][1],ntypes)
+for i in range(nbonds): ntypes = max(bond[i][1],ntypes)
 ntypes = int(ntypes)
 ncount = ntypes * [0]
 bin = nbins * [0]
-for i in xrange(nbins): 
+for i in range(nbins):
   bin[i] = ntypes * [0]
 
 # read snapshots one-at-a-time
@@ -72,7 +71,7 @@ while 1:
   d.sort()
   x,y,z = d.vecs(time,"x","y","z")
 
-  for i in xrange(nbonds):
+  for i in range(nbonds):
 
     delx = x[jatom[i]] - x[iatom[i]]
     dely = y[jatom[i]] - y[iatom[i]]
@@ -101,22 +100,22 @@ while 1:
       bin[ibin][btype[i]] += nbins
       ncount[btype[i]] += 1
     else:
-      print "Warning: bond distance outside specified range"
+      print("Warning: bond distance outside specified range")
-      print "Bond type:", btype[i]+1
+      print("Bond type:", btype[i]+1)
-      print "Bond number:", i
+      print("Bond number:", i)
-  print time,    
+  print(time, end=' ')
 
-print
+print()
-print "Printing bond distance normalized distribution to",outfile
+print("Printing bond distance normalized distribution to",outfile)
 
 fp = open(outfile,"w")
 rrange = rmax - rmin
-for i in xrange(nbins):
+for i in range(nbins):
-  print >>fp, rmin + rrange*float(i)/float(nbins), 
+  print(rmin + rrange*float(i)/float(nbins), end=' ', file=fp)
-  for j in xrange(ntypes):
+  for j in range(ntypes):
     if (ncount[j] > 0):
-      print >>fp, float(bin[i][j])/float(ncount[j])/rrange,
+      print(float(bin[i][j])/float(ncount[j])/rrange, end=' ', file=fp)
     else:
-      print >>fp, 0.0,    
+      print(0.0, end=' ', file=fp)
-  print >>fp 
+  print(file=fp)
 fp.close()

scripts/clogview.py

@@ -15,18 +15,18 @@ from clog import clog
 from plotview import plotview
 from gnu import gnu
 from matlab import matlab
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 3:
-  raise StandardError, "Syntax: clogview.py gnu/matlab files  ..."
+  raise Exception("Syntax: clogview.py gnu/matlab files  ...")
 
 style = argv[1]
 files = ' '.join(argv[2:])
 
 c = clog(files)
-exec "plot = %s()" % style
+exec("plot = %s()" % style)
 p = plotview(c,plot)
 p.x = "Time"
 

scripts/cluster.py

@@ -18,7 +18,7 @@
 import sys
 from dump import dump
 from gnu import gnu
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
@@ -62,7 +62,7 @@ def distance(atom1,atom2,box):
 # main script
 
 if len(argv) < 6:
-  raise StandardError,"cluster.py type1 type2 cutoff nbin dump.1 dump.2 ..."
+  raise Exception("cluster.py type1 type2 cutoff nbin dump.1 dump.2 ...")
 
 type1 = int(argv[1])
 type2 = int(argv[2])
@@ -81,20 +81,20 @@ d.aselect.test("$type == %d or $type == %d" % (type1,type2))
 cutsq = cutoff*cutoff
 cluster = nbin*[0]
 
-print "Clustering ..."
+print("Clustering ...")
 
 flag = 0
 while 1:
   which,time,flag = d.iterator(flag)
   if flag == -1: break
   time,box,atoms,bonds,tris = d.viz(which)
-  print time,
+  print(time, end=' ')
   sys.stdout.flush()
 
   # loop over all type1 atoms
 
   n = len(atoms)
-  for i in xrange(n):
+  for i in range(n):
     itype = atoms[i][1]
     if itype != type1: continue
     ncount = 0
@@ -102,7 +102,7 @@ while 1:
     # loop over all type2 atoms
     # increment cluster count if distance is within cutoff
 
-    for j in xrange(n):
+    for j in range(n):
       jtype = atoms[j][1]
       if jtype != type2 or i == j: continue
       distsq = distance(atoms[i],atoms[j],box)
@@ -113,9 +113,9 @@ while 1:
     if ncount >= nbin: cluster[nbin-1] += 1
     else: cluster[ncount] += 1
 
-print
+print()
-print "Cluster size and count:"
+print("Cluster size and count:")
-for i in range(nbin): print i,cluster[i]
+for i in range(nbin): print(i,cluster[i])
 
 # comment out if don't want plot
 

scripts/density.py

@@ -14,12 +14,12 @@
 
 import sys
 from dump import dump
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 5:
-  raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..."
+  raise Exception("Syntax: density.py x/y/z nbin outfile files ...")
 
 direction = argv[1]
 nbins = int(argv[2])
@@ -41,7 +41,7 @@ while 1:
     tmp,ntypes = d.minmax("type")
     ntypes = int(ntypes)
     bin = nbins * [0]
-    for i in xrange(nbins): bin[i] = ntypes * [0]
+    for i in range(nbins): bin[i] = ntypes * [0]
     first = 0
 
   box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo,
@@ -52,26 +52,26 @@ while 1:
   elif direction == "y": type,x = d.vecs(time,"type","y")
   elif direction == "z": type,x = d.vecs(time,"type","z")
 
-  type = map(int,type)
+  type = list(map(int,type))
   natoms = len(type)
-  for i in xrange(natoms): type[i] -= 1
+  for i in range(natoms): type[i] -= 1
 
-  for i in xrange(natoms):
+  for i in range(natoms):
     ibin = int(nbins*x[i] + 0.5)
     if (ibin < 0): ibin += nbins
     if (ibin > nbins-1): ibin -= nbins
     bin[ibin][type[i]] += nbins/vol
   nsnaps += 1
-  print time,
+  print(time, end=' ')
 
-print
+print()
-print "Printing ", direction, "-directional density distribution in mol/L to",outfile
+print("Printing ", direction, "-directional density distribution in mol/L to",outfile)
 conversion = 1660.53873              # convert from atoms/Angs^3 to mol/L
 
 fp = open(outfile,"w")
-for i in xrange(nbins):
+for i in range(nbins):
-  print >>fp, float(i)/float(nbins), 
+  print(float(i)/float(nbins), end=' ', file=fp)
-  for j in xrange(ntypes):
+  for j in range(ntypes):
-    print >>fp, conversion*bin[i][j]/nsnaps,
+    print(conversion*bin[i][j]/nsnaps, end=' ', file=fp)
-  print >>fp 
+  print(file=fp)
 fp.close()

scripts/density2d.py

@@ -18,12 +18,12 @@
 import sys
 import numpy as np
 from dump import dump
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 5:
-    raise StandardError, "Syntax: density.py x/y/z nbin vmin vmax outfile files ..."
+    raise Exception("Syntax: density.py x/y/z nbin vmin vmax outfile files ...")
 
 direction = argv[1]
 nbins = int(argv[2])
@@ -102,11 +102,11 @@ while 1:
         zmin = max(zmin,box[0])
     vol = dx * dy * float(zmax - zmin)
 
-    type = map(int,type)
+    type = list(map(int,type))
     natoms = len(type)
-    for i in xrange(natoms): type[i] -= 1
+    for i in range(natoms): type[i] -= 1
 
-    for i in xrange(natoms):
+    for i in range(natoms):
         ibin = int(nbins*x[i])
         jbin = int(nbins*y[i])
         zloc = float(z[i])*float(dz)
@@ -117,10 +117,10 @@ while 1:
         if (jbin > nbins-1): jbin = nbins - 1
         bin[jbin][ibin][type[i]] += nbins*nbins/vol
     nsnaps += 1
-    print time,
+    print(time, end=' ')
 
-print 
+print()
-print "Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile)
+print("Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile))
 conversion = 1660.53873  # convert from atoms/Angs^3 to mol/L
 
 fp = open(outfile,"w")
@@ -129,10 +129,10 @@ fp = open(outfile,"w")
 # for k in xrange(ntypes):
 #     print >>fp, " %8s " %(k),
 # print >>fp
-for i in xrange(nbins):
+for i in range(nbins):
-    for j in xrange(nbins):
+    for j in range(nbins):
-        print >>fp, " %8.3f  %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)),
+        print(" %8.3f  %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)), end=' ', file=fp)
-        for k in xrange(ntypes):
+        for k in range(ntypes):
-            print >>fp, " %8.3f " % (conversion*bin[j][i][k]/nsnaps),
+            print(" %8.3f " % (conversion*bin[j][i][k]/nsnaps), end=' ', file=fp)
-        print >>fp 
+        print(file=fp)
 fp.close()

scripts/density_area.py

@@ -16,12 +16,12 @@
 
 import sys
 from dump import dump
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 5:
-  raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..."
+  raise Exception("Syntax: density.py x/y/z nbin outfile files ...")
 
 direction = argv[1]
 nbins = int(argv[2])
@@ -44,7 +44,7 @@ while 1:
     tmp,ntypes = d.minmax("type")
     ntypes = int(ntypes)
     bin = nbins * [0]
-    for i in xrange(nbins): bin[i] = ntypes * [0]
+    for i in range(nbins): bin[i] = ntypes * [0]
     first = 0
 
   box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo,
@@ -55,21 +55,21 @@ while 1:
   elif direction == "y": type,x = d.vecs(time,"type","y")
   elif direction == "z": type,x = d.vecs(time,"type","z")
 
-  type = map(int,type)
+  type = list(map(int,type))
   natoms = len(type)
-  for i in xrange(natoms): type[i] -= 1
+  for i in range(natoms): type[i] -= 1
 
-  for i in xrange(natoms):
+  for i in range(natoms):
     ibin = int(nbins*x[i] + 0.5)
     if (ibin < 0): ibin += nbins
     if (ibin > nbins-1): ibin -= nbins
     bin[ibin][type[i]] += nbins/vol
   nsnaps += 1
-  print time,
+  print(time, end=' ')
 
-print
+print()
-print "Printing ",direction,"-directional density distribution in mol/L to", \
+print("Printing ",direction,"-directional density distribution in mol/L to", \
-      outfile
+      outfile)
 conversion = 1660.53873              # convert from atoms/Angs^3 to mol/L
 
 # Output as x, density_1, area_1, ...
@@ -78,20 +78,20 @@ fp = open(outfile,"w")
 first = 1
 xden = nbins * [0]
 yden = nbins * [0]
-for i in xrange(nbins): yden[i] = ntypes * [0]
+for i in range(nbins): yden[i] = ntypes * [0]
 sum = ntypes * [0]
-for i in xrange(nbins):
+for i in range(nbins):
   xden[i] = float(i)/float(nbins)
-  print >>fp, xden[i],
+  print(xden[i], end=' ', file=fp)
   if first:
-    for j in xrange(ntypes):
+    for j in range(ntypes):
       yden[i][j] = conversion*bin[i][j]/nsnaps
-      print >>fp, yden[i][j], sum[j],
+      print(yden[i][j], sum[j], end=' ', file=fp)
     first = 0
   else:
-    for j in xrange(ntypes):
+    for j in range(ntypes):
       yden[i][j] = conversion*bin[i][j]/nsnaps
       sum[j] += 0.5 * (xden[i] - xden[i-1]) * (yden[i][j] + yden[i-1][j])
-      print >>fp, yden[i][j], sum[j],
+      print(yden[i][j], sum[j], end=' ', file=fp)
-  print >>fp 
+  print(file=fp)
 fp.close()

scripts/distance.py

@@ -12,12 +12,12 @@
 from math import sqrt
 
 if len(argv) < 3:
-  raise StandardError,"distance.py maxcut dump.file1 dump.file2 ..."
+  raise Exception("distance.py maxcut dump.file1 dump.file2 ...")
 
 maxcut = float(argv[1])
 maxcut_sq = maxcut*maxcut
 
-files = ' '.join(argv[2:])		        # dump files
+files = ' '.join(argv[2:])                      # dump files
 d = dump(files,0)
 d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
 
@@ -36,8 +36,8 @@ while 1:
   yprd = box[4] - box[1]
   zprd = box[5] - box[2]
 
-  for i in xrange(n):
+  for i in range(n):
-    for j in xrange(i+1,n):
+    for j in range(i+1,n):
 
       delx = x[j] - x[i]
       if abs(delx) > 0.5*xprd:
@@ -65,11 +65,11 @@ while 1:
           rsq = delx*delx + dely*dely + delz*delz
 
           if rsq < maxcut_sq:
-            print "time = %d, id[i] = %d, id[j] = %d," \
+            print("time = %d, id[i] = %d, id[j] = %d," \
                " type[i] = %d, type[j] = %d, distance = %g" % \
-              (time, id[i], id[j], type[i], type[j], sqrt(rsq))
+              (time, id[i], id[j], type[i], type[j], sqrt(rsq)))
 
   d.tselect.none()
   d.tselect.one(time)
-  print "timestep = ", time
+  print("timestep = ", time)
   d.delete()

scripts/dview.py

@@ -10,7 +10,7 @@
 # main script
 
 if len(argv) < 2:
-  raise StandardError, "Syntax: dview.py dump.1 ..."
+  raise Exception("Syntax: dview.py dump.1 ...")
 
 files = ' '.join(argv[1:])
 

scripts/dview_standalone.py

@@ -13,18 +13,18 @@ import sys
 from dump import dump
 
 # w/out Pizza.py these lines need to come before import of gl tool
-import Tkinter
+import tkinter
-tkroot = Tkinter.Tk()
+tkroot = tkinter.Tk()
 tkroot.withdraw()
 
 from gl import gl
 from vcr import vcr
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 2:
-  raise StandardError, "Syntax: dview.py dump.1 ..."
+  raise Exception("Syntax: dview.py dump.1 ...")
 
 files = ' '.join(argv[1:])
 

scripts/flux.py

@@ -14,12 +14,12 @@
 
 import sys
 from dump import dump
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 5:
-  raise StandardError, "Syntax: flux.py x/y/z plane outfile files ..."
+  raise Exception("Syntax: flux.py x/y/z plane outfile files ...")
 
 direction = argv[1]
 scaled_plane = float(argv[2])
@@ -58,7 +58,7 @@ while 1:
   prd = hi - lo
   plane = lo + scaled_plane*prd
 
-  print time,
+  print(time, end=' ')
   sys.stdout.flush()
 
   natoms = len(x)
@@ -67,7 +67,7 @@ while 1:
 
   typeflux = ntypes * [0]
 
-  for i in xrange(natoms):
+  for i in range(natoms):
     id[i] = int(id[i])
     type[i] = int(type[i])
     if jconfig == 1: x_initial[id[i]] = x[i]
@@ -78,10 +78,10 @@ while 1:
        crossings = int((plane - x[i])/prd) + 1
        typeflux[type[i]] -= crossings
 
-  print >>f,time,
+  print(time, end=' ', file=f)
-  for j in xrange(ntypes-1):
+  for j in range(ntypes-1):
-    print >>f,typeflux[j+1],
+    print(typeflux[j+1], end=' ', file=f)
-  print >>f
+  print(file=f)
-print
+print()
 
 f.close()

scripts/iview.py

@@ -11,10 +11,10 @@
 
 import sys
 from animate import animate
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 # this could be done with one-line alias in shell start-up file
 
-if len(argv) < 2: raise StandardError, "Syntax: iview.py files  ..."
+if len(argv) < 2: raise Exception("Syntax: iview.py files  ...")
 a = animate(' '.join(argv[1:]))

scripts/logview.py

@@ -15,17 +15,17 @@ from log import log
 from plotview import plotview
 from gnu import gnu
 from matlab import matlab
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 3:
-  raise StandardError, "Syntax: logview.py gnu/matlab files  ..."
+  raise Exception("Syntax: logview.py gnu/matlab files  ...")
 
 style = argv[1]
 files = ' '.join(argv[2:])
 
 lg = log(files)
-exec "plot = %s()" % style
+exec("plot = %s()" % style)
 p = plotview(lg,plot)
 

scripts/movie.py

@@ -4,7 +4,7 @@
 # Purpose: create images from LAMMPS dump snapshots
 # Syntax:  movie.py raster/svg theta phi dump.1 dump.2 ...
 #          raster/svg = style of image to create
-#	   theta/phi = vertical (z) and azimuthal angle to view from
+#          theta/phi = vertical (z) and azimuthal angle to view from
 #          files = one or more dump files
 # Example: movie.py svg 60 130 dump.*
 # Author:  Steve Plimpton (Sandia)
@@ -15,12 +15,12 @@ import sys
 from dump import dump
 from raster import raster
 from svg import svg
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) < 5:
-  raise StandardError, "Syntax: movie.py raster/svg theta phi dump.1 ..."
+  raise Exception("Syntax: movie.py raster/svg theta phi dump.1 ...")
 
 style = argv[1]
 theta = float(argv[2])
@@ -28,6 +28,6 @@ phi = float(argv[3])
 files = ' '.join(argv[4:])
 
 d = dump(files)
-exec "viz = %s(d)" % style
+exec("viz = %s(d)" % style)
 viz.rotate(theta,phi)
 viz.all()

scripts/plot.py

@@ -14,17 +14,17 @@ import sys
 from plotview import plotview
 from gnu import gnu
 from matlab import matlab
-if not globals().has_key("argv"): argv = sys.argv
+if "argv" not in globals(): argv = sys.argv
 
 # main script
 
 if len(argv) != 3:
-  raise StandardError, "Syntax: plot.py gnu/matlab file"
+  raise Exception("Syntax: plot.py gnu/matlab file")
 
 style = argv[1]
 file = argv[2]
 
 v = vec(file)
-exec "plot = %s()" % style
+exec("plot = %s()" % style)
 p = plotview(v,plot)
 

src/animate.py

@@ -8,23 +8,33 @@
 
 # animate tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, os, re, glob
+try:
+  from Tkinter import *
+except ImportError:
+  from tkinter import *
+
 oneline = "Animate a series of image files"
 
 docstr = """
 a = animate("image*.png")     create GUI to animate set of image files
+a = animate("image*.png",1)   2nd arg = sort filenames, 0 = no sort, def = 1
 
 Actions (same as GUI widgets):
 
-a.first()		      go to first frame
+a.first()                     go to first frame
 a.prev()                      go to previous frame
 a.back()                      play backwards from current frame to start
-a.stop()         	      stop on current frame		
+a.stop()                      stop on current frame
 a.play()                      play from current frame to end
-a.next()		      go to next frame
+a.next()                      go to next frame
-a.last()		      go to last frame
+a.last()                      go to last frame
 
-a.frame(31)    	              set frame slider
+a.frame(31)                   set frame slider
-a.delay(0.4)     	      set delay slider
+a.delay(0.4)                  set delay slider
 """
 
 # History
@@ -45,11 +55,6 @@ a.delay(0.4)     	      set delay slider
 #   delay_value = delay between frames (secs)
 #   delay_msec = delay in millisec
 
-# Imports and external programs
-
-import sys, os, commands, re, glob
-from Tkinter import *
-from ImageTk import PhotoImage
 
 # Class definition
 
@@ -57,23 +62,24 @@ class animate:
 
   # --------------------------------------------------------------------
 
-  def __init__(self,filestr):
+  def __init__(self,filestr,sortflag=1):
     self.loop_flag = 0
     self.delay_value = 0.0
     self.delay_msec = 0
 
     # convert filestr into full list of files
 
-    list = str.split(filestr)
+    flist = str.split(filestr)
     self.files = []
-    for file in list: self.files += glob.glob(file)
+    for file in flist: self.files += glob.glob(file)
     self.nframes = len(self.files)
-    if self.nframes == 0: raise StandardError, "No files to load"
+    if self.nframes == 0: raise Exception("No files to load")
+    if sortflag: self.files.sort()
 
     # load all images
 
     self.images = []
-    for i in xrange(self.nframes):
+    for i in range(self.nframes):
       self.images.append(PhotoImage(file=self.files[i]))
 
     # grab Tk instance from main

src/bdump.py

@@ -8,18 +8,25 @@
 
 # bdump tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, types
+import functools
+from os import popen
+
 oneline = "Read dump files with bond info"
 
 docstr = """
 b = bdump("dump.one")             read in one or more dump files
-b = bdump("dump.1 dump.2.gz")	  can be gzipped
+b = bdump("dump.1 dump.2.gz")     can be gzipped
-b = bdump("dump.*")		  wildcard expands to multiple files
+b = bdump("dump.*")               wildcard expands to multiple files
-b = bdump("dump.*",0)		  two args = store filenames, but don't read
+b = bdump("dump.*",0)             two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
   no column name assignment is performed
 
-time = b.next()             	  read next snapshot from dump files
+time = b.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -60,11 +67,6 @@ time,box,atoms,bonds,tris,lines = b.viz(index)   return list of viz objects
 #     natoms = # of atoms
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
-# Imports and external programs
-
-import sys, commands, re, glob, types
-from os import popen
-
 try:
     import numpy as np
     oldnumeric = False
@@ -92,7 +94,7 @@ class bdump:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no bdump file specified"
+      raise Exception("no bdump file specified")
 
     if len(list) == 1:
       self.increment = 0
@@ -117,26 +119,26 @@ class bdump:
       snap = self.read_snapshot(f)
       while snap:
         self.snaps.append(snap)
-        print snap.time,
+        print(snap.time, end=' ')
         sys.stdout.flush()
         snap = self.read_snapshot(f)
 
       f.close()
-    print
+    print()
 
     # sort entries by timestep, cull duplicates
 
-    self.snaps.sort(self.compare_time)
+    self.snaps.sort(key = functools.cmp_to_key(self.compare_time))
     self.cull()
     self.nsnaps = len(self.snaps)
-    print "read %d snapshots" % self.nsnaps
+    print("read %d snapshots" % self.nsnaps)
 
   # --------------------------------------------------------------------
   # read next snapshot from list of files
 
   def next(self):
 
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     # read next snapshot in current file using eof as pointer
     # if fail, try next file
@@ -148,15 +150,15 @@ class bdump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
+        self.eof = 0
-	continue
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     self.snaps.append(snap)
@@ -183,14 +185,14 @@ class bdump:
       if snap.natoms:
         words = f.readline().split()
         ncol = len(words)
-        for i in xrange(1,snap.natoms):
+        for i in range(1,snap.natoms):
           words += f.readline().split()
-        floats = map(float,words)
+        floats = list(map(float,words))
         if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
         else: atoms = np.zeros((snap.natoms,ncol),np.float)
         start = 0
         stop = ncol
-        for i in xrange(snap.natoms):
+        for i in range(snap.natoms):
           atoms[i] = floats[start:stop]
           start = stop
           stop += ncol
@@ -205,7 +207,7 @@ class bdump:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "bdump map() requires pairs of mappings"
+      raise Exception("bdump map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -269,7 +271,7 @@ class bdump:
     # abs() of type since could be negative
 
     bonds = []
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       atom = snap.atoms[i]
       bonds.append([int(atom[id]),abs(int(atom[type])),
                     int(atom[atom1]),int(atom[atom2])])

src/cfg.py

@@ -8,10 +8,15 @@
 
 # cfg tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys
+
 oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
 
 docstr = """
-c = cfg(d)		d = object containing atom coords (dump, data)
+c = cfg(d)              d = object containing atom coords (dump, data)
 
 c.one()                 write all snapshots to tmp.cfg
 c.one("new")            write all snapshots to new.cfg
@@ -34,10 +39,6 @@ c.single(N,"file")      write snapshot for timestep N to file.cfg
 # Variables
 #   data = data file to read from
 
-# Imports and external programs
-
-import sys
-
 # Class definition
 
 class cfg:
@@ -65,18 +66,18 @@ class cfg:
       ylen = box[4]-box[1]
       zlen = box[5]-box[2]
 
-      print >>f,"Number of particles = %d " % len(atoms)
+      print("Number of particles = %d " % len(atoms), file=f)
-      print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
+      print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
-      print >>f,"H0(1,1) = %20.10f A " % xlen
+      print("H0(1,1) = %20.10f A " % xlen, file=f)
-      print >>f,"H0(1,2) = 0.0 A " 
+      print("H0(1,2) = 0.0 A ", file=f)
-      print >>f,"H0(1,3) = 0.0 A " 
+      print("H0(1,3) = 0.0 A ", file=f)
-      print >>f,"H0(2,1) = 0.0 A " 
+      print("H0(2,1) = 0.0 A ", file=f)
-      print >>f,"H0(2,2) = %20.10f A " % ylen
+      print("H0(2,2) = %20.10f A " % ylen, file=f)
-      print >>f,"H0(2,3) = 0.0 A " 
+      print("H0(2,3) = 0.0 A ", file=f)
-      print >>f,"H0(3,1) = 0.0 A " 
+      print("H0(3,1) = 0.0 A ", file=f)
-      print >>f,"H0(3,2) = 0.0 A " 
+      print("H0(3,2) = 0.0 A ", file=f)
-      print >>f,"H0(3,3) = %20.10f A " % zlen
+      print("H0(3,3) = %20.10f A " % zlen, file=f)
-      print >>f,"#"
+      print("#", file=f)
 
       for atom in atoms:
         itype = int(atom[1])
@@ -84,14 +85,14 @@ class cfg:
         yfrac = (atom[3]-box[1])/ylen
         zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
-        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
+        print("1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
     f.close()
-    print "\nwrote %d snapshots to %s in CFG format" % (n,file)
+    print("\nwrote %d snapshots to %s in CFG format" % (n,file))
 
   # --------------------------------------------------------------------
 
@@ -120,18 +121,18 @@ class cfg:
       ylen = box[4]-box[1]
       zlen = box[5]-box[2]
 
-      print >>f,"Number of particles = %d " % len(atoms)
+      print("Number of particles = %d " % len(atoms), file=f)
-      print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
+      print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
-      print >>f,"H0(1,1) = %20.10f A " % xlen
+      print("H0(1,1) = %20.10f A " % xlen, file=f)
-      print >>f,"H0(1,2) = 0.0 A " 
+      print("H0(1,2) = 0.0 A ", file=f)
-      print >>f,"H0(1,3) = 0.0 A " 
+      print("H0(1,3) = 0.0 A ", file=f)
-      print >>f,"H0(2,1) = 0.0 A " 
+      print("H0(2,1) = 0.0 A ", file=f)
-      print >>f,"H0(2,2) = %20.10f A " % ylen
+      print("H0(2,2) = %20.10f A " % ylen, file=f)
-      print >>f,"H0(2,3) = 0.0 A " 
+      print("H0(2,3) = 0.0 A ", file=f)
-      print >>f,"H0(3,1) = 0.0 A " 
+      print("H0(3,1) = 0.0 A ", file=f)
-      print >>f,"H0(3,2) = 0.0 A " 
+      print("H0(3,2) = 0.0 A ", file=f)
-      print >>f,"H0(3,3) = %20.10f A " % zlen
+      print("H0(3,3) = %20.10f A " % zlen, file=f)
-      print >>f,"#"
+      print("#", file=f)
 
       for atom in atoms:
         itype = int(atom[1])
@@ -139,14 +140,14 @@ class cfg:
         yfrac = (atom[3]-box[1])/ylen
         zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
-        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
+        print("1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       f.close()
       n += 1
 
-    print "\nwrote %s snapshots in CFG format" % n
+    print("\nwrote %s snapshots in CFG format" % n)
 
   # --------------------------------------------------------------------
 
@@ -163,18 +164,18 @@ class cfg:
     ylen = box[4]-box[1]
     zlen = box[5]-box[2]
 
-    print >>f,"Number of particles = %d " % len(atoms)
+    print("Number of particles = %d " % len(atoms), file=f)
-    print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
+    print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
-    print >>f,"H0(1,1) = %20.10f A " % xlen
+    print("H0(1,1) = %20.10f A " % xlen, file=f)
-    print >>f,"H0(1,2) = 0.0 A " 
+    print("H0(1,2) = 0.0 A ", file=f)
-    print >>f,"H0(1,3) = 0.0 A " 
+    print("H0(1,3) = 0.0 A ", file=f)
-    print >>f,"H0(2,1) = 0.0 A " 
+    print("H0(2,1) = 0.0 A ", file=f)
-    print >>f,"H0(2,2) = %20.10f A " % ylen
+    print("H0(2,2) = %20.10f A " % ylen, file=f)
-    print >>f,"H0(2,3) = 0.0 A " 
+    print("H0(2,3) = 0.0 A ", file=f)
-    print >>f,"H0(3,1) = 0.0 A " 
+    print("H0(3,1) = 0.0 A ", file=f)
-    print >>f,"H0(3,2) = 0.0 A " 
+    print("H0(3,2) = 0.0 A ", file=f)
-    print >>f,"H0(3,3) = %20.10f A " % zlen
+    print("H0(3,3) = %20.10f A " % zlen, file=f)
-    print >>f,"#"
+    print("#", file=f)
 
     for atom in atoms:
       itype = int(atom[1])
@@ -182,6 +183,6 @@ class cfg:
       yfrac = (atom[3]-box[1])/ylen
       zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
-      print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
+      print("1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
 
     f.close()

src/chain.py

@@ -8,15 +8,21 @@
 
 # chain tool
 
+# Imports and external programs
+
+from __future__ import print_function, division, absolute_import
+import math
+from data import data
+
 oneline = "Create bead-spring chains for LAMMPS input"
 
 docstr = """
 c = chain(N,rho)            setup box with N monomers at reduced density rho
-c = chain(N,rho,1,1,2)	    x,y,z = aspect ratio of box (def = 1,1,1)
+c = chain(N,rho,1,1,2)      x,y,z = aspect ratio of box (def = 1,1,1)
 
 c.seed = 48379              set random # seed (def = 12345)
-c.mtype = 2    		    set type of monomers (def = 1)
+c.mtype = 2                 set type of monomers (def = 1)
-c.btype = 1           	    set type of bonds (def = 1)
+c.btype = 1                 set type of bonds (def = 1)
 c.blen = 0.97               set length of bonds (def = 0.97)
 c.dmin = 1.02               set min dist from i-1 to i+1 site (def = 1.02)
 
@@ -24,7 +30,7 @@ c.id = "chain"              set molecule ID to chain # (default)
 c.id = "end1"               set molecule ID to count from one end of chain
 c.id = "end2"               set molecule ID to count from either end of chain
 
-c.build(100,10)		    create 100 chains, each of length 10
+c.build(100,10)             create 100 chains, each of length 10
 
   can be invoked multiple times interleaved with different settings
   must fill box with total of N monomers
@@ -52,11 +58,6 @@ c.write("data.file")        write out all built chains to LAMMPS data file
 #   xlo,ylo,zlo = -xyz prd / 2
 #   xhi,yhi,zhi = x,y,zprd /2
 
-# Imports and external programs
-
-import math
-from data import data
-
 # Class definition
 
 class chain:
@@ -92,12 +93,12 @@ class chain:
     self.zlo = -self.zprd/2.0
     self.zhi = self.zprd/2.0
 
-    print "Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd)
+    print("Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd))
 
   # --------------------------------------------------------------------
 
   def build(self,n,nper):
-    for ichain in xrange(n):
+    for ichain in range(n):
       atoms = []
       bonds = []
       id_atom_prev = id_mol_prev = id_bond_prev = 0
@@ -107,12 +108,12 @@ class chain:
       if len(self.bonds):
         id_bond_prev = self.bonds[-1][0]
 
-      for imonomer in xrange(nper):
+      for imonomer in range(nper):
         if imonomer == 0:
           x = self.xlo + self.random()*self.xprd
           y = self.ylo + self.random()*self.yprd
           z = self.zlo + self.random()*self.zprd
-	  ix = iy = iz = 0
+          ix = iy = iz = 0
         else:
           restriction = True
           while restriction:
@@ -143,14 +144,14 @@ class chain:
           idmol = imonomer + 1
         elif self.id == "end2":
           idmol = imonomer + 1
-          if idmol > nper/2:
+          if idmol > nper//2:
             idmol = nper - imonomer
         else:
-          raise StandardError,"chain ID is not a valid value"
+          raise Exception("chain ID is not a valid value")
 
         atoms.append([idatom,idmol,self.mtype,x,y,z,ix,iy,iz])
         if imonomer:
-	  bondid = id_bond_prev + imonomer
+          bondid = id_bond_prev + imonomer
           bonds.append([bondid,self.btype,idatom-1,idatom])
 
       self.atoms += atoms
@@ -160,16 +161,16 @@ class chain:
 
   def write(self,file):
     if len(self.atoms) != self.n:
-      raise StandardError,"%d monomers instead of requested %d" % \
+      raise Exception("%d monomers instead of requested %d" % \
-                           (len(self.atoms),self.n)
+                           (len(self.atoms),self.n))
 
-    list = [atom[2] for atom in self.atoms]
+    atlist = [atom[2] for atom in self.atoms]
-    atypes = max(list)
+    atypes = max(atlist)
 
     btypes = 0
     if len(self.bonds):
-      list = [bond[1] for bond in self.bonds]
+      btlist = [bond[1] for bond in self.bonds]
-      btypes = max(list)
+      btypes = max(btlist)
 
     # create the data file
 
@@ -229,7 +230,7 @@ class chain:
   # --------------------------------------------------------------------
 
   def random(self):
-    k = self.seed/IQ
+    k = self.seed//IQ
     self.seed = IA*(self.seed-k*IQ) - IR*k
     if self.seed < 0:
       self.seed += IM

src/clog.py

@@ -8,6 +8,12 @@
 
 # clog tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob
+from os import popen
+
 oneline = "Read ChemCell and SPPARKS log files and extract time-series data"
 
 docstr = """
@@ -26,7 +32,7 @@ nvec = c.nvec                        # of vectors of thermo info
 nlen = c.nlen                        length of each vectors
 names = c.names                      list of vector names
 a,b,... = c.get("A","B",...)         return one or more vectors of values
-c.write("file.txt")	 	     write all vectors to a file
+c.write("file.txt")                  write all vectors to a file
 c.write("file.txt","A","B",...)      write listed vectors to a file
 
   get and write allow abbreviated (uniquely) vector names
@@ -46,11 +52,6 @@ c.write("file.txt","A","B",...)      write listed vectors to a file
 #   data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1
 #   firststr = string that begins a time-series section in log file
 
-# Imports and external programs
-
-import sys, re, glob
-from os import popen
-
 try: tmp = PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
 
@@ -74,7 +75,7 @@ class clog:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no log file specified"
+      raise Exception("no log file specified")
 
     if len(list) > 1 and len(list[1]): self.firststr = list[1]
     if len(list) == 3: self.ave = 1
@@ -86,12 +87,12 @@ class clog:
 
   def read_all(self):
     self.read_header(self.flist[0])
-    if self.nvec == 0: raise StandardError,"log file has no values"
+    if self.nvec == 0: raise Exception("log file has no values")
 
     # read all files
 
     for file in self.flist: self.read_one(file)
-    print
+    print()
 
     # if no average, sort entries by timestep, cull duplicates
     # if average, call self.average()
@@ -102,33 +103,33 @@ class clog:
     else: self.average()
 
     self.nlen = len(self.data)
-    print "read %d log entries" % self.nlen
+    print("read %d log entries" % self.nlen)
 
   # --------------------------------------------------------------------
 
   def get(self,*keys):
     if len(keys) == 0:
-      raise StandardError, "no log vectors specified"
+      raise Exception("no log vectors specified")
 
     map = []
     for key in keys:
-      if self.ptr.has_key(key):
+      if key in self.ptr:
         map.append(self.ptr[key])
       else:
         count = 0
         for i in range(self.nvec):
-	  if self.names[i].find(key) == 0:
+          if self.names[i].find(key) == 0:
-	    count += 1
+            count += 1
-	    index = i
+            index = i
         if count == 1:
           map.append(index)
         else:
-          raise StandardError, "unique log vector %s not found" % key
+          raise Exception("unique log vector %s not found" % key)
 
     vecs = []
     for i in range(len(keys)):
       vecs.append(self.nlen * [0])
-      for j in xrange(self.nlen):
+      for j in range(self.nlen):
         vecs[i][j] = self.data[j][map[i]]
 
     if len(keys) == 1: return vecs[0]
@@ -140,26 +141,26 @@ class clog:
     if len(keys):
       map = []
       for key in keys:
-        if self.ptr.has_key(key):
+        if key in self.ptr:
           map.append(self.ptr[key])
         else:
           count = 0
           for i in range(self.nvec):
-	    if self.names[i].find(key) == 0:
+            if self.names[i].find(key) == 0:
-	      count += 1
+              count += 1
-	      index = i
+              index = i
           if count == 1:
             map.append(index)
           else:
-            raise StandardError, "unique log vector %s not found" % key
+            raise Exception("unique log vector %s not found" % key)
     else:
-      map = range(self.nvec)
+      map = list(range(self.nvec))
 
     f = open(filename,"w")
-    for i in xrange(self.nlen):
+    for i in range(self.nlen):
-      for j in xrange(len(map)):
+      for j in range(len(map)):
-        print >>f,self.data[i][map[j]],
+        print(self.data[i][map[j]], end=' ', file=f)
-      print >>f
+      print(file=f)
     f.close()
 
   # --------------------------------------------------------------------
@@ -195,12 +196,12 @@ class clog:
         data.append(self.nvec*[0])
         nlen += 1
       counts[j] += 1
-      for m in xrange(self.nvec): data[j][m] += self.data[i][m]
+      for m in range(self.nvec): data[j][m] += self.data[i][m]
       j += 1
       i += 1
 
-    for i in xrange(nlen):
+    for i in range(nlen):
-      for j in xrange(self.nvec):
+      for j in range(self.nvec):
         data[i][j] /= counts[j]
 
     self.nlen = nlen
@@ -261,26 +262,26 @@ class clog:
       elif s1 >= 0 and s2 >= 0 and s2 < s1:  # found s1,s2 with s2 before s1
         s1 = 0
       elif s1 == -1 and s2 >= 0:             # found s2, but no s1
-	last = 1
+        last = 1
         s1 = 0
       elif s1 >= 0 and s2 == -1:             # found s1, but no s2
         last = 1
         s1 = txt.find("\n",s1) + 1
         s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
+        eof -= len(txt) - s2
       elif s1 == -1 and s2 == -1:            # found neither
                                              # could be end-of-file section
-					     # or entire read was one chunk
+                                             # or entire read was one chunk
 
         if txt.find("Loop time of",start) == start:   # end of file, so exit
-	  eof -= len(txt) - start                     # reset eof to "Loop"
+          eof -= len(txt) - start                     # reset eof to "Loop"
-	  break
+          break
 
-	last = 1                                      # entire read is a chunk
+        last = 1                                      # entire read is a chunk
         s1 = 0
         s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
+        eof -= len(txt) - s2
-	if s1 == s2: break
+        if s1 == s2: break
 
       chunk = txt[s1:s2-1]
       start = s2
@@ -291,11 +292,11 @@ class clog:
       lines = chunk.split("\n")
       for line in lines:
         words = line.split()
-        self.data.append(map(float,words))
+        self.data.append(list(map(float,words)))
 
       # print last timestep of chunk
 
-      print int(self.data[len(self.data)-1][0]),
+      print(int(self.data[len(self.data)-1][0]), end=' ')
       sys.stdout.flush()
 
     return eof

src/data.py

@@ -8,11 +8,16 @@
 
 # data tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+from os import popen
+
 oneline = "Read, write, manipulate LAMMPS data files"
 
 docstr = """
 d = data("data.poly")            read a LAMMPS data file, can be gzipped
-d = data()			 create an empty data file
+d = data()                       create an empty data file
 
 d.map(1,"id",3,"x")              assign names to atom columns (1-N)
 
@@ -26,13 +31,13 @@ d.reorder("Atoms",1,3,2,4,5)     reorder columns (1-N) in a data file section
 
   1,3,2,4,5 = new order of previous columns, can delete columns this way
 
-d.title = "My LAMMPS data file"	 set title of the data file
+d.title = "My LAMMPS data file"  set title of the data file
 d.headers["atoms"] = 1500        set a header value
 d.sections["Bonds"] = lines      set a section to list of lines (with newlines)
-d.delete("bonds")		 delete a keyword or section of data file
+d.delete("bonds")                delete a keyword or section of data file
 d.delete("Bonds")
-d.replace("Atoms",5,vec)      	 replace Nth column of section with vector
+d.replace("Atoms",5,vec)         replace Nth column of section with vector
-d.newxyz(dmp,1000)		 replace xyz in Atoms with xyz of snapshot N
+d.newxyz(dmp,1000)               replace xyz in Atoms with xyz of snapshot N
 
   newxyz assumes id,x,y,z are defined in both data and dump files
     also replaces ix,iy,iz if they are defined
@@ -70,10 +75,6 @@ d.write("data.new")             write a LAMMPS data file
 #   sections = dictionary with section name as key, array of lines as values
 #   nselect = 1 = # of snapshots
 
-# Imports and external programs
-
-from os import popen
-
 try: tmp = PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
 
@@ -109,16 +110,16 @@ class data:
       found = 0
       for keyword in hkeywords:
         if line.find(keyword) >= 0:
-	  found = 1
+          found = 1
-	  words = line.split()
+          words = line.split()
-	  if keyword == "xlo xhi" or keyword == "ylo yhi" or \
+          if keyword == "xlo xhi" or keyword == "ylo yhi" or \
-	    keyword == "zlo zhi":
+            keyword == "zlo zhi":
-	    headers[keyword] = (float(words[0]),float(words[1]))
+            headers[keyword] = (float(words[0]),float(words[1]))
-	  elif keyword == "xy xz yz":
+          elif keyword == "xy xz yz":
-	    headers[keyword] = \
+            headers[keyword] = \
               (float(words[0]),float(words[1]),float(words[2]))
           else:
-	    headers[keyword] = int(words[0])
+            headers[keyword] = int(words[0])
       if not found:
         break
 
@@ -128,16 +129,15 @@ class data:
       for pair in skeywords:
         keyword,length = pair[0],pair[1]
         if keyword == line:
-	  found = 1
+          found = 1
-          if not headers.has_key(length):
+          if length not in headers:
-            raise StandardError, \
+            raise Exception("data section %s has no matching header value" % line)
-                  "data section %s has no matching header value" % line
+          f.readline()
-	  f.readline()
           list = []
-          for i in xrange(headers[length]): list.append(f.readline())
+          for i in range(headers[length]): list.append(f.readline())
           sections[keyword] = list
       if not found:
-        raise StandardError,"invalid section %s in data file" % line
+        raise Exception("invalid section %s in data file" % line)
       f.readline()
       line = f.readline()
       if not line:
@@ -153,7 +153,7 @@ class data:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "data map() requires pairs of mappings"
+      raise Exception("data map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -161,19 +161,19 @@ class data:
   # --------------------------------------------------------------------
   # extract info from data file fields
 
-  def get(self,*list):
+  def get(self,*flist):
-    if len(list) == 1:
+    if len(flist) == 1:
-      field = list[0]
+      field = flist[0]
       array = []
       lines = self.sections[field]
       for line in lines:
         words = line.split()
-        values = map(float,words)
+        values = list(map(float,words))
         array.append(values)
       return array
-    elif len(list) == 2:
+    elif len(flist) == 2:
-      field = list[0]
+      field = flist[0]
-      n = list[1] - 1
+      n = flist[1] - 1
       vec = []
       lines = self.sections[field]
       for line in lines:
@@ -181,7 +181,7 @@ class data:
         vec.append(float(words[n]))
       return vec
     else:
-      raise StandardError, "invalid arguments for data.get()"
+      raise Exception("invalid arguments for data.get()")
 
   # --------------------------------------------------------------------
   # reorder columns in a data file field
@@ -192,10 +192,10 @@ class data:
     oldlines = self.sections[name]
     newlines = natoms*[""]
     for index in order:
-      for i in xrange(len(newlines)):
+      for i in range(len(newlines)):
         words = oldlines[i].split()
         newlines[i] += words[index-1] + " "
-    for i in xrange(len(newlines)):
+    for i in range(len(newlines)):
       newlines[i] += "\n"
     self.sections[name] = newlines
 
@@ -206,7 +206,7 @@ class data:
     lines = self.sections[name]
     newlines = []
     j = icol - 1
-    for i in xrange(len(lines)):
+    for i in range(len(lines)):
       line = lines[i]
       words = line.split()
       words[j] = str(vector[i])
@@ -222,19 +222,15 @@ class data:
   def newxyz(self,dm,ntime):
     nsnap = dm.findtime(ntime)
 
-    if dm.scaled(nsnap): scaleflag = 1
-    else: scaleflag = 0
     dm.sort(ntime)
 
-    if scaleflag: dm.unscale(ntime)
     x,y,z = dm.vecs(ntime,"x","y","z")
-    if scaleflag: dm.scale(ntime)
 
     self.replace("Atoms",self.names['x']+1,x)
     self.replace("Atoms",self.names['y']+1,y)
     self.replace("Atoms",self.names['z']+1,z)
 
-    if dm.names.has_key("ix") and self.names.has_key("ix"):
+    if "ix" in dm.names and "ix" in self.names:
       ix,iy,iz = dm.vecs(ntime,"ix","iy","iz")
       self.replace("Atoms",self.names['ix']+1,ix)
       self.replace("Atoms",self.names['iy']+1,iy)
@@ -245,33 +241,33 @@ class data:
 
   def delete(self,keyword):
 
-    if self.headers.has_key(keyword): del self.headers[keyword]
+    if keyword in self.headers: del self.headers[keyword]
-    elif self.sections.has_key(keyword): del self.sections[keyword]
+    elif keyword in self.sections: del self.sections[keyword]
-    else: raise StandardError, "keyword not found in data object"
+    else: raise Exception("keyword not found in data object")
 
   # --------------------------------------------------------------------
   # write out a LAMMPS data file
 
   def write(self,file):
     f = open(file,"w")
-    print >>f,self.title
+    print(self.title, file=f)
     for keyword in hkeywords:
-      if self.headers.has_key(keyword):
+      if keyword in self.headers:
         if keyword == "xlo xhi" or keyword == "ylo yhi" or \
                keyword == "zlo zhi":
-	  pair = self.headers[keyword]
+          pair = self.headers[keyword]
-	  print >>f,pair[0],pair[1],keyword
+          print(pair[0],pair[1],keyword, file=f)
         elif keyword == "xy xz yz":
-	  triple = self.headers[keyword]
+          triple = self.headers[keyword]
-	  print >>f,triple[0],triple[1],triple[2],keyword
+          print(triple[0],triple[1],triple[2],keyword, file=f)
         else:
-	  print >>f,self.headers[keyword],keyword
+          print(self.headers[keyword],keyword, file=f)
     for pair in skeywords:
       keyword = pair[0]
-      if self.sections.has_key(keyword):
+      if keyword in self.sections:
-        print >>f,"\n%s\n" % keyword
+        print("\n%s\n" % keyword, file=f)
         for line in self.sections[keyword]:
-	  print >>f,line,
+          print(line, end=' ', file=f)
     f.close()
 
   # --------------------------------------------------------------------
@@ -286,13 +282,13 @@ class data:
 
   def findtime(self,n):
     if n == 0: return 0
-    raise StandardError, "no step %d exists" % (n)
+    raise Exception("no step %d exists" % (n))
 
   # --------------------------------------------------------------------
   # return list of atoms and bonds to viz for data object
 
   def viz(self,isnap):
-    if isnap: raise StandardError, "cannot call data.viz() with isnap != 0"
+    if isnap: raise Exception("cannot call data.viz() with isnap != 0")
 
     id = self.names["id"]
     type = self.names["type"]
@@ -318,7 +314,7 @@ class data:
     # assumes atoms are sorted so can lookup up the 2 atoms in each bond
 
     bonds = []
-    if self.sections.has_key("Bonds"):
+    if "Bonds" in self.sections:
       bondlines = self.sections["Bonds"]
       for line in bondlines:
         words = line.split()
@@ -331,7 +327,7 @@ class data:
                       float(atom1words[z]),
                       float(atom2words[x]),float(atom2words[y]),
                       float(atom2words[z]),
-		      float(atom1words[type]),float(atom2words[type])])
+                      float(atom1words[type]),float(atom2words[type])])
 
     tris = []
     lines = []
@@ -357,18 +353,18 @@ class data:
 
 hkeywords = ["atoms","lines","tris",
              "bonds","angles","dihedrals","impropers",
-	     "atom types","bond types","angle types","dihedral types",
+             "atom types","bond types","angle types","dihedral types",
-	     "improper types","xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
+             "improper types","xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
 
 skeywords = [["Masses","atom types"],
              ["Atoms","atoms"],["Lines","lines"],["Triangles","tris"],
              ["Bonds","bonds"],
-	     ["Angles","angles"],["Dihedrals","dihedrals"],
+             ["Angles","angles"],["Dihedrals","dihedrals"],
-	     ["Impropers","impropers"],["Velocities","atoms"],
+             ["Impropers","impropers"],["Velocities","atoms"],
              ["Pair Coeffs","atom types"],
-	     ["Bond Coeffs","bond types"],["Angle Coeffs","angle types"],
+             ["Bond Coeffs","bond types"],["Angle Coeffs","angle types"],
-	     ["Dihedral Coeffs","dihedral types"],
+             ["Dihedral Coeffs","dihedral types"],
-	     ["Improper Coeffs","improper types"],
+             ["Improper Coeffs","improper types"],
              ["BondBond Coeffs","angle types"],
              ["BondAngle Coeffs","angle types"],
              ["MiddleBondTorsion Coeffs","dihedral types"],

src/dump.py

@@ -8,19 +8,28 @@
 
 # dump tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, types
+from os import popen
+from math import *             # any function could be used by set()
+import os
+import functools
+
 oneline = "Read, write, manipulate dump files and particle attributes"
 
 docstr = """
 d = dump("dump.one")              read in one or more dump files
-d = dump("dump.1 dump.2.gz")	  can be gzipped
+d = dump("dump.1 dump.2.gz")      can be gzipped
-d = dump("dump.*")		  wildcard expands to multiple files
+d = dump("dump.*")                wildcard expands to multiple files
-d = dump("dump.*",0)		  two args = store filenames, but don't read
+d = dump("dump.*",0)              two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
   if atoms have 5 or 8 columns, assign id,type,x,y,z (ix,iy,iz)
   atoms will be unscaled if stored in files as scaled
 
-time = d.next()             	  read next snapshot from dump files
+time = d.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -32,20 +41,20 @@ d.map(1,"id",3,"x")               assign names to atom columns (1-N)
 
   not needed if dump file is self-describing
 
-d.tselect.all()			  select all timesteps
+d.tselect.all()                   select all timesteps
-d.tselect.one(N)		  select only timestep N
+d.tselect.one(N)                  select only timestep N
-d.tselect.none()		  deselect all timesteps
+d.tselect.none()                  deselect all timesteps
-d.tselect.skip(M)		  select every Mth step
+d.tselect.skip(M)                 select every Mth step
 d.tselect.test("$t >= 100 and $t < 10000")      select matching timesteps
-d.delete()	      	      	  delete non-selected timesteps
+d.delete()                        delete non-selected timesteps
 
   selecting a timestep also selects all atoms in the timestep
   skip() and test() only select from currently selected timesteps
   test() uses a Python Boolean expression with $t for timestep value
     Python comparison syntax: == != < > <= >= and or
 
-d.aselect.all()	      	                      select all atoms in all steps
+d.aselect.all()                               select all atoms in all steps
-d.aselect.all(N)      	                      select all atoms in one step
+d.aselect.all(N)                              select all atoms in one step
 d.aselect.test("$id > 100 and $type == 2")    select match atoms in all steps
 d.aselect.test("$id > 100 and $type == 2",N)  select matching atoms in one step
 
@@ -56,24 +65,24 @@ d.aselect.test("$id > 100 and $type == 2",N)  select matching atoms in one step
     Python comparison syntax: == != < > <= >= and or
     $name must end with a space
 
-d.write("file")	   	           write selected steps/atoms to dump file
+d.write("file")                    write selected steps/atoms to dump file
-d.write("file",head,app)	   write selected steps/atoms to dump file
+d.write("file",head,app)           write selected steps/atoms to dump file
-d.scatter("tmp")		   write selected steps/atoms to multiple files
+d.scatter("tmp")                   write selected steps/atoms to multiple files
 
   write() can be specified with 2 additional flags
-    headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
+    head = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
   scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc
 
-d.scale() 	    	  	   scale x,y,z to 0-1 for all timesteps
+d.scale()                          scale x,y,z to 0-1 for all timesteps
-d.scale(100)			   scale atom coords for timestep N
+d.scale(100)                       scale atom coords for timestep N
-d.unscale()			   unscale x,y,z to box size to all timesteps
+d.unscale()                        unscale x,y,z to box size to all timesteps
-d.unscale(1000)			   unscale atom coords for timestep N
+d.unscale(1000)                    unscale atom coords for timestep N
-d.wrap()			   wrap x,y,z into periodic box via ix,iy,iz
+d.wrap()                           wrap x,y,z into periodic box via ix,iy,iz
-d.unwrap()			   unwrap x,y,z out of box via ix,iy,iz
+d.unwrap()                         unwrap x,y,z out of box via ix,iy,iz
-d.owrap("other")		   wrap x,y,z to same image as another atom
+d.owrap("other")                   wrap x,y,z to same image as another atom
-d.sort()              	  	   sort atoms by atom ID in all selected steps
+d.sort()                           sort atoms by atom ID in all selected steps
-d.sort("x")            	  	   sort atoms by column value in all steps
+d.sort("x")                        sort atoms by column value in all steps
-d.sort(1000)			   sort atoms in timestep N
+d.sort(1000)                       sort atoms in timestep N
 
   scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
   wrap(), unwrap(), owrap() require ix,iy,iz be defined
@@ -85,8 +94,8 @@ d.sort(1000)			   sort atoms in timestep N
 m1,m2 = d.minmax("type")               find min/max values for a column
 d.set("$ke = $vx * $vx + $vy * $vy")   set a column to a computed value
 d.setv("type",vector)                  set a column to a vector of values
-d.spread("ke",N,"color")	       2nd col = N ints spread over 1st col
+d.spread("ke",N,"color")               2nd col = N ints spread over 1st col
-d.clone(1000,"color")	       	       clone timestep N values to other steps
+d.clone(1000,"color")                  clone timestep N values to other steps
 
   minmax() operates on selected timesteps and atoms
   set() operates on selected timesteps and atoms
@@ -107,7 +116,7 @@ d.clone(1000,"color")	       	       clone timestep N values to other steps
     values at every timestep are set to value at timestep N for that atom ID
     useful for propagating a color map
 
-t = d.time()  	     	       	   return vector of selected timestep values
+t = d.time()                       return vector of selected timestep values
 fx,fy,... = d.atom(100,"fx","fy",...)   return vector(s) for atom ID N
 fx,fy,... = d.vecs(1000,"fx","fy",...)  return vector(s) for timestep N
 
@@ -117,7 +126,7 @@ fx,fy,... = d.vecs(1000,"fx","fy",...)  return vector(s) for timestep N
 index,time,flag = d.iterator(0/1)          loop over dump snapshots
 time,box,atoms,bonds,tris,lines = d.viz(index)   return list of viz objects
 d.atype = "color"                          set column returned as "type" by viz
-d.extra(obj)				   extract bond/tri/line info from obj
+d.extra(obj)                               extract bond/tri/line info from obj
 
   iterator() loops over selected timesteps
   iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
@@ -180,19 +189,12 @@ d.extra(obj)				   extract bond/tri/line info from obj
 #     xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
-# Imports and external programs
-
-import sys, commands, re, glob, types
-from os import popen
-from math import *             # any function could be used by set()
-import os
-
 try:
-    import numpy as np
+  import numpy as np
-    oldnumeric = False
+  oldnumeric = False
 except:
-    import Numeric as np
+  import Numeric as np
-    oldnumeric = True
+  oldnumeric = True
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -228,7 +230,7 @@ class dump:
       # check whether to output or not
       if "debugMode" in dictionary: outputfl = dictionary["debugMode"]
 
-      if outputfl: print "number of subprocess:", os.getpid()
+      if outputfl: print("number of subprocess:", os.getpid())
 
       self.flist = dictionary["filelist"]
       self.multiprocflag = 1
@@ -240,7 +242,7 @@ class dump:
       self.flist = []
       for word in words: self.flist += glob.glob(word)
       if len(self.flist) == 0 and len(input) == 1:
-        raise StandardError,"no dump file specified"
+        raise Exception("no dump file specified")
 
       if len(input) == 1:
         self.increment = 0
@@ -261,31 +263,32 @@ class dump:
     outputfl = True
     if "output" in kwargs: outputfl = kwargs["output"]
 
-    if outputfl: print "reading dump file..."
+    if outputfl: print("reading dump file...")
 
     for i, file in enumerate(self.flist):
       if file[-3:] == ".gz":
         f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
-      else: f = open(file)
+      else:
+        f = open(file)
 
       snap = self.read_snapshot(f)
       while snap:
         self.snaps.append(snap)
-        if outputfl: print snap.time,
+        if outputfl: print(snap.time,end=' ')
         self.fileNums.append(snap.time)
         sys.stdout.flush()
         snap = self.read_snapshot(f)
 
       f.close()
-    if outputfl: print
+    if outputfl: print()
 
     # sort entries by timestep, cull duplicates
 
-    self.snaps.sort(self.compare_time)
+    self.snaps.sort(key = functools.cmp_to_key(self.compare_time))
     self.fileNums.sort()
     self.cull()
     self.nsnaps = len(self.snaps)
-    #print "read %d snapshots" % self.nsnaps
+    #print("read %d snapshots" % self.nsnaps)
 
     # select all timesteps and atoms
 
@@ -294,32 +297,32 @@ class dump:
     # set default names for atom columns if file wasn't self-describing
 
     if len(self.snaps) == 0:
-      if outputfl: print "no column assignments made"
+      if outputfl: print("no column assignments made")
     elif len(self.names):
-      if outputfl: print "assigned columns:",self.names2str()
+      if outputfl: print("assigned columns:",self.names2str())
     else:
-      if outputfl: print "no column assignments made"
+      if outputfl: print("no column assignments made")
       pass
 
     # if snapshots are scaled, unscale them
 
-    if (not self.names.has_key("x")) or \
+    if ("x" not in self.names) or \
-       (not self.names.has_key("y")) or \
+       ("y" not in self.names) or \
-       (not self.names.has_key("z")):
+       ("z" not in self.names):
-      print "dump scaling status is unknown"
+      print("dump scaling status is unknown")
     elif self.nsnaps > 0:
       if self.scale_original == 1: self.unscale()
       elif self.scale_original == 0:
-        if outputfl: print "dump is already unscaled"
+        if outputfl: print("dump is already unscaled")
       else:
-        if outputfl: print "dump scaling status is unknown"
+        if outputfl: print("dump scaling status is unknown")
 
   # --------------------------------------------------------------------
   # read next snapshot from list of files
 
   def next(self):
 
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     # read next snapshot in current file using eof as pointer
     # if fail, try next file
@@ -331,24 +334,25 @@ class dump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
+        self.eof = 0
-	continue
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     # select the new snapshot with all its atoms
 
     self.snaps.append(snap)
+    self.fileNums.append(snap.time)
     snap = self.snaps[self.nsnaps]
     snap.tselect = 1
     snap.nselect = snap.natoms
-    for i in xrange(snap.natoms): snap.aselect[i] = 1
+    for i in range(snap.natoms): snap.aselect[i] = 1
     self.nsnaps += 1
     self.nselect += 1
 
@@ -411,14 +415,14 @@ class dump:
       if snap.natoms:
         words = f.readline().split()
         ncol = len(words)
-        for i in xrange(1,snap.natoms):
+        for i in range(1,snap.natoms):
           words += f.readline().split()
-        floats = map(float,words)
+        floats = list(map(float,words))
         if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
         else: atoms = np.zeros((snap.natoms,ncol),np.float)
         start = 0
         stop = ncol
-        for i in xrange(snap.natoms):
+        for i in range(snap.natoms):
           atoms[i] = floats[start:stop]
           start = stop
           stop += ncol
@@ -433,7 +437,7 @@ class dump:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "dump map() requires pairs of mappings"
+      raise Exception("dump map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -445,25 +449,26 @@ class dump:
     ndel = i = 0
     while i < self.nsnaps:
       if not self.snaps[i].tselect:
+        del self.fileNums[i]
         del self.snaps[i]
         self.nsnaps -= 1
         ndel += 1
       else: i += 1
-    print "%d snapshots deleted" % ndel
+    print("%d snapshots deleted" % ndel)
-    print "%d snapshots remaining" % self.nsnaps
+    print("%d snapshots remaining" % self.nsnaps)
 
   # --------------------------------------------------------------------
   # scale coords to 0-1 for all snapshots or just one
 
-  def scale(self,*list):
+  def scale(self,*dumplist):
-    if len(list) == 0:
+    if len(dumplist) == 0:
-      print "Scaling dump ..."
+      print("Scaling dump ...")
       x = self.names["x"]
       y = self.names["y"]
       z = self.names["z"]
       for snap in self.snaps: self.scale_one(snap,x,y,z)
     else:
-      i = self.findtime(list[0])
+      i = self.findtime(dumplist[0])
       x = self.names["x"]
       y = self.names["y"]
       z = self.names["z"]
@@ -483,15 +488,15 @@ class dump:
   # --------------------------------------------------------------------
   # unscale coords from 0-1 to box size for all snapshots or just one
 
-  def unscale(self,*list):
+  def unscale(self,*dumplist):
-    if len(list) == 0:
+    if len(dumplist) == 0:
-      print "Unscaling dump ..."
+      print("Unscaling dump ...")
       x = self.names["x"]
       y = self.names["y"]
       z = self.names["z"]
       for snap in self.snaps: self.unscale_one(snap,x,y,z)
     else:
-      i = self.findtime(list[0])
+      i = self.findtime(dumplist[0])
       x = self.names["x"]
       y = self.names["y"]
       z = self.names["z"]
@@ -512,7 +517,7 @@ class dump:
   # wrap coords from outside box to inside
 
   def wrap(self):
-    print "Wrapping dump ..."
+    print("Wrapping dump ...")
 
     x = self.names["x"]
     y = self.names["y"]
@@ -534,7 +539,7 @@ class dump:
   # unwrap coords from inside box to outside
 
   def unwrap(self):
-    print "Unwrapping dump ..."
+    print("Unwrapping dump ...")
 
     x = self.names["x"]
     y = self.names["y"]
@@ -557,7 +562,7 @@ class dump:
   # if dynamic extra lines or triangles defined, owrap them as well
 
   def owrap(self,other):
-    print "Wrapping to other ..."
+    print("Wrapping to other ...")
 
     id = self.names["id"]
     x = self.names["x"]
@@ -574,9 +579,9 @@ class dump:
       zprd = snap.zhi - snap.zlo
       atoms = snap.atoms
       ids = {}
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         ids[atoms[i][id]] = i
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         j = ids[atoms[i][iother]]
         atoms[i][x] += (atoms[i][ix]-atoms[j][ix])*xprd
         atoms[i][y] += (atoms[i][iy]-atoms[j][iy])*yprd
@@ -589,11 +594,11 @@ class dump:
   # convert column names assignment to a string, in column order
 
   def names2str(self):
-    ncol = max(self.names.values()) #len(self.snaps[0].atoms[0])
+    pairs = list(self.names.items())
-    pairs = self.names.items()
+    values = list(self.names.values())
-    values = self.names.values()
+    ncol = len(pairs)
     str = ""
-    for i in xrange(ncol):
+    for i in range(ncol):
       if i in values: str += pairs[values.index(i)][0] + ' '
     return str
 
@@ -602,24 +607,24 @@ class dump:
   # if arg = string, sort all steps by that column
   # if arg = numeric, sort atoms in single step
 
-  def sort(self,*list, **kwargs):
+  def sort(self,*tslist, **kwargs):
 
     # check whether to output or not
     outputfl = True
     if "output" in kwargs: outputfl = kwargs["output"]
 
-    if len(list) == 0:
+    if len(tslist) == 0:
-      if outputfl: print "Sorting selected snapshots ..."
+      if outputfl: print("Sorting selected snapshots ...")
       id = self.names["id"]
       for snap in self.snaps:
         if snap.tselect: self.sort_one(snap,id)
-    elif type(list[0]) is types.StringType:
+    elif isinstance(tslist[0], str):
-      if outputfl: print "Sorting selected snapshots by %s ..." % list[0]
+      if outputfl: print("Sorting selected snapshots by %s ..." % tslist[0])
-      id = self.names[list[0]]
+      id = self.names[tslist[0]]
       for snap in self.snaps:
         if snap.tselect: self.sort_one(snap,id)
     else:
-      i = self.findtime(list[0])
+      i = self.findtime(tslist[0])
       id = self.names["id"]
       self.sort_one(self.snaps[i],id)
 
@@ -630,7 +635,7 @@ class dump:
     atoms = snap.atoms
     ids = atoms[:,id]
     ordering = np.argsort(ids)
-    for i in xrange(len(atoms[0])):
+    for i in range(len(atoms[0])):
       atoms[:,i] = np.take(atoms[:,i],ordering)
 
   # --------------------------------------------------------------------
@@ -642,33 +647,33 @@ class dump:
     else: f = open(file,"a")
     for snap in self.snaps:
       if not snap.tselect: continue
-      print snap.time,
+      print(snap.time, end=' ')
       sys.stdout.flush()
 
       if header:
-        print >>f,"ITEM: TIMESTEP"
+        print("ITEM: TIMESTEP", file=f)
-        print >>f,snap.time
+        print(snap.time, file=f)
-        print >>f,"ITEM: NUMBER OF ATOMS"
+        print("ITEM: NUMBER OF ATOMS", file=f)
-        print >>f,snap.nselect
+        print(snap.nselect, file=f)
-        print >>f,"ITEM: BOX BOUNDS"
+        print("ITEM: BOX BOUNDS", file=f)
-        print >>f,snap.xlo,snap.xhi
+        print(snap.xlo,snap.xhi, file=f)
-        print >>f,snap.ylo,snap.yhi
+        print(snap.ylo,snap.yhi, file=f)
-        print >>f,snap.zlo,snap.zhi
+        print(snap.zlo,snap.zhi, file=f)
-        print >>f,"ITEM: ATOMS",namestr
+        print("ITEM: ATOMS",namestr, file=f)
 
       atoms = snap.atoms
       nvalues = len(atoms[0])
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         line = ""
-        for j in xrange(nvalues):
+        for j in range(nvalues):
           if (j < 2):
             line += str(int(atoms[i][j])) + " "
           else:
             line += str(atoms[i][j]) + " "
-        print >>f,line
+        print(line, file=f)
     f.close()
-    print "\n%d snapshots" % self.nselect
+    print("\n%d snapshots" % self.nselect)
 
   # --------------------------------------------------------------------
   # write one dump file per snapshot from current selection
@@ -677,34 +682,34 @@ class dump:
     if len(self.snaps): namestr = self.names2str()
     for snap in self.snaps:
       if not snap.tselect: continue
-      print snap.time,
+      print(snap.time, end=' ')
       sys.stdout.flush()
 
       file = root + "." + str(snap.time)
       f = open(file,"w")
-      print >>f,"ITEM: TIMESTEP"
+      print("ITEM: TIMESTEP", file=f)
-      print >>f,snap.time
+      print(snap.time, file=f)
-      print >>f,"ITEM: NUMBER OF ATOMS"
+      print("ITEM: NUMBER OF ATOMS", file=f)
-      print >>f,snap.nselect
+      print(snap.nselect, file=f)
-      print >>f,"ITEM: BOX BOUNDS"
+      print("ITEM: BOX BOUNDS", file=f)
-      print >>f,snap.xlo,snap.xhi
+      print(snap.xlo,snap.xhi, file=f)
-      print >>f,snap.ylo,snap.yhi
+      print(snap.ylo,snap.yhi, file=f)
-      print >>f,snap.zlo,snap.zhi
+      print(snap.zlo,snap.zhi, file=f)
-      print >>f,"ITEM: ATOMS",namestr
+      print("ITEM: ATOMS",namestr, file=f)
 
       atoms = snap.atoms
       nvalues = len(atoms[0])
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         line = ""
-        for j in xrange(nvalues):
+        for j in range(nvalues):
           if (j < 2):
             line += str(int(atoms[i][j])) + " "
           else:
             line += str(atoms[i][j]) + " "
-        print >>f,line
+        print(line, file=f)
       f.close()
-    print "\n%d snapshots" % self.nselect
+    print("\n%d snapshots" % self.nselect)
 
   # --------------------------------------------------------------------
   # find min/max across all selected snapshots/atoms for a particular column
@@ -716,7 +721,7 @@ class dump:
     for snap in self.snaps:
       if not snap.tselect: continue
       atoms = snap.atoms
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         if atoms[i][icol] < min: min = atoms[i][icol]
         if atoms[i][icol] > max: max = atoms[i][icol]
@@ -726,15 +731,15 @@ class dump:
   # set a column value via an equation for all selected snapshots
 
   def set(self,eq):
-    print "Setting ..."
+    print("Setting ...")
     pattern = "\$\w*"
-    list = re.findall(pattern,eq)
+    eqlist = re.findall(pattern,eq)
 
-    lhs = list[0][1:]
+    lhs = eqlist[0][1:]
-    if not self.names.has_key(lhs):
+    if lhs not in self.names:
       self.newcolumn(lhs)
 
-    for item in list:
+    for item in eqlist:
       name = item[1:]
       column = self.names[name]
       insert = "snap.atoms[i][%d]" % (column)
@@ -743,25 +748,25 @@ class dump:
 
     for snap in self.snaps:
       if not snap.tselect: continue
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
-        if snap.aselect[i]: exec ceq
+        if snap.aselect[i]: exec(ceq)
 
   # --------------------------------------------------------------------
   # set a column value via an input vec for all selected snapshots/atoms
 
   def setv(self,colname,vec):
-    print "Setting ..."
+    print("Setting ...")
-    if not self.names.has_key(colname):
+    if colname not in self.names:
       self.newcolumn(colname)
     icol = self.names[colname]
 
     for snap in self.snaps:
       if not snap.tselect: continue
       if snap.nselect != len(vec):
-        raise StandardError,"vec length does not match # of selected atoms"
+        raise Exception("vec length does not match # of selected atoms")
       atoms = snap.atoms
       m = 0
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if snap.aselect[i]:
           atoms[i][icol] = vec[m]
           m += 1
@@ -774,12 +779,12 @@ class dump:
     icol = self.names[col]
     id = self.names["id"]
     ids = {}
-    for i in xrange(self.snaps[istep].natoms):
+    for i in range(self.snaps[istep].natoms):
       ids[self.snaps[istep].atoms[i][id]] = i
     for snap in self.snaps:
       if not snap.tselect: continue
       atoms = snap.atoms
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         j = ids[atoms[i][id]]
         atoms[i][icol] = self.snaps[istep].atoms[j][icol]
@@ -789,18 +794,18 @@ class dump:
 
   def spread(self,old,n,new):
     iold = self.names[old]
-    if not self.names.has_key(new): self.newcolumn(new)
+    if new not in self.names: self.newcolumn(new)
     inew = self.names[new]
 
     min,max = self.minmax(old)
-    print "min/max = ",min,max
+    print("min/max = ",min,max)
 
     gap = max - min
     invdelta = n/gap
     for snap in self.snaps:
       if not snap.tselect: continue
       atoms = snap.atoms
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         ivalue = int((atoms[i][iold] - min) * invdelta) + 1
         if ivalue > n: ivalue = n
@@ -822,12 +827,12 @@ class dump:
   # --------------------------------------------------------------------
   # extract vector(s) of values for atom ID n at each selected timestep
 
-  def atom(self,n,*list):
+  def atom(self,n,*tslist):
-    if len(list) == 0:
+    if len(tslist) == 0:
-      raise StandardError, "no columns specified"
+      raise Exception("no columns specified")
     columns = []
     values = []
-    for name in list:
+    for name in tslist:
       columns.append(self.names[name])
       values.append(self.nselect * [0])
     ncol = len(columns)
@@ -837,40 +842,40 @@ class dump:
     for snap in self.snaps:
       if not snap.tselect: continue
       atoms = snap.atoms
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if atoms[i][id] == n: break
       if atoms[i][id] != n:
-        raise StandardError, "could not find atom ID in snapshot"
+        raise Exception("could not find atom ID in snapshot")
-      for j in xrange(ncol):
+      for j in range(ncol):
         values[j][m] = atoms[i][columns[j]]
       m += 1
 
-    if len(list) == 1: return values[0]
+    if len(tslist) == 1: return values[0]
     else: return values
 
   # --------------------------------------------------------------------
   # extract vector(s) of values for selected atoms at chosen timestep
 
-  def vecs(self,n,*list):
+  def vecs(self,n,*tslist):
     snap = self.snaps[self.findtime(n)]
 
-    if len(list) == 0:
+    if len(tslist) == 0:
-      raise StandardError, "no columns specified"
+      raise Exception("no columns specified")
     columns = []
     values = []
-    for name in list:
+    for name in tslist:
       columns.append(self.names[name])
       values.append(snap.nselect * [0])
     ncol = len(columns)
 
     m = 0
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       if not snap.aselect[i]: continue
-      for j in xrange(ncol):
+      for j in range(ncol):
         values[j][m] = snap.atoms[i][columns[j]]
       m += 1
 
-    if len(list) == 1: return values[0]
+    if len(tslist) == 1: return values[0]
     else: return values
 
   # --------------------------------------------------------------------
@@ -915,7 +920,7 @@ class dump:
   def iterator(self,flag):
     start = 0
     if flag: start = self.iterate + 1
-    for i in xrange(start,self.nsnaps):
+    for i in range(start,self.nsnaps):
       if self.snaps[i].tselect:
         self.iterate = i
         return i,self.snaps[i].time,1
@@ -951,7 +956,7 @@ class dump:
     # need Numeric/Numpy mode here
 
     atoms = []
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       if not snap.aselect[i]: continue
       atom = snap.atoms[i]
       atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]])
@@ -970,7 +975,7 @@ class dump:
       elif self.bondflag == 2:
         tmp1,tmp2,tmp3,bondlist,tmp4,tmp5 = self.objextra.viz(time,1)
       alist = {}
-      for i in xrange(len(atoms)): alist[int(atoms[i][0])] = i
+      for i in range(len(atoms)): alist[int(atoms[i][0])] = i
       for bond in bondlist:
         try:
           i = alist[bond[2]]
@@ -1004,9 +1009,9 @@ class dump:
   # --------------------------------------------------------------------
 
   def findtime(self,n):
-    for i in xrange(self.nsnaps):
+    for i in range(self.nsnaps):
       if self.snaps[i].time == n: return i
-    raise StandardError, "no step %d exists" % n
+    raise Exception("no step %d exists" % n)
 
   # --------------------------------------------------------------------
   # return maximum box size across all selected snapshots
@@ -1033,7 +1038,7 @@ class dump:
     for snap in self.snaps:
       if not snap.tselect: continue
       atoms = snap.atoms
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
         if atoms[i][icol] > max: max = atoms[i][icol]
     return int(max)
@@ -1046,7 +1051,7 @@ class dump:
 
     # data object, grab bonds statically
 
-    if type(arg) is types.InstanceType and ".data" in str(arg.__class__):
+    if isinstance(arg, object) and ".data" in str(arg.__class__):
       self.bondflag = 0
       try:
         bondlist = []
@@ -1059,11 +1064,11 @@ class dump:
           self.bondflag = 1
           self.bondlist = bondlist
       except:
-        raise StandardError,"could not extract bonds from data object"
+        raise Exception("could not extract bonds from data object")
 
     # cdata object, grab tris and lines statically
 
-    elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
+    elif isinstance(arg, object) and ".cdata" in str(arg.__class__):
       self.triflag = self.lineflag = 0
       try:
         tmp,tmp,tmp,tmp,tris,lines = arg.viz(0)
@@ -1074,34 +1079,34 @@ class dump:
           self.lineflag = 1
           self.linelist = lines
       except:
-        raise StandardError,"could not extract tris/lines from cdata object"
+        raise Exception("could not extract tris/lines from cdata object")
 
     # mdump object, grab tris dynamically
 
-    elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
+    elif isinstance(arg, object) and ".mdump" in str(arg.__class__):
       self.triflag = 2
       self.objextra = arg
 
     # bdump object, grab bonds dynamically
 
-    elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__):
+    elif isinstance(arg, object) and ".bdump" in str(arg.__class__):
       self.bondflag = 2
       self.objextra = arg
 
     # ldump object, grab tris dynamically
 
-    elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__):
+    elif isinstance(arg, object) and ".ldump" in str(arg.__class__):
       self.lineflag = 2
       self.objextra = arg
 
     # tdump object, grab tris dynamically
 
-    elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__):
+    elif isinstance(arg, object) and ".tdump" in str(arg.__class__):
       self.triflag = 2
       self.objextra = arg
 
     else:
-      raise StandardError,"unrecognized argument to dump.extra()"
+      raise Exception("unrecognized argument to dump.extra()")
 
   # --------------------------------------------------------------------
 
@@ -1140,7 +1145,7 @@ class tselect:
       snap.tselect = 1
     data.nselect = len(data.snaps)
     data.aselect.all()
-    if outputfl: print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    if outputfl: print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -1152,7 +1157,7 @@ class tselect:
     data.snaps[i].tselect = 1
     data.nselect = 1
     data.aselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -1161,7 +1166,7 @@ class tselect:
     for snap in data.snaps:
       snap.tselect = 0
     data.nselect = 0
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -1177,7 +1182,7 @@ class tselect:
       snap.tselect = 0
       data.nselect -= 1
     data.aselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -1186,14 +1191,16 @@ class tselect:
     snaps = data.snaps
     cmd = "flag = " + teststr.replace("$t","snaps[i].time")
     ccmd = compile(cmd,'','single')
-    for i in xrange(data.nsnaps):
+    for i in range(data.nsnaps):
       if not snaps[i].tselect: continue
-      exec ccmd
+      ldict = {'data':data,'snaps':snaps,'i':i}
+      exec(ccmd,globals(),ldict)
+      flag = ldict['flag']
       if not flag:
         snaps[i].tselect = 0
         data.nselect -= 1
     data.aselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
 # --------------------------------------------------------------------
 # atom selection class
@@ -1210,12 +1217,12 @@ class aselect:
     if len(args) == 0:                           # all selected timesteps
       for snap in data.snaps:
         if not snap.tselect: continue
-        for i in xrange(snap.natoms): snap.aselect[i] = 1
+        for i in range(snap.natoms): snap.aselect[i] = 1
         snap.nselect = snap.natoms
     else:                                        # one timestep
       n = data.findtime(args[0])
       snap = data.snaps[n]
-      for i in xrange(snap.natoms): snap.aselect[i] = 1
+      for i in range(snap.natoms): snap.aselect[i] = 1
       snap.nselect = snap.natoms
 
   # --------------------------------------------------------------------
@@ -1226,8 +1233,8 @@ class aselect:
     # replace all $var with snap.atoms references and compile test string
 
     pattern = "\$\w*"
-    list = re.findall(pattern,teststr)
+    testlist = re.findall(pattern,teststr)
-    for item in list:
+    for item in testlist:
       name = item[1:]
       column = data.names[name]
       insert = "snap.atoms[i][%d]" % column
@@ -1238,29 +1245,33 @@ class aselect:
     if len(args) == 0:                           # all selected timesteps
       for snap in data.snaps:
         if not snap.tselect: continue
-        for i in xrange(snap.natoms):
+        for i in range(snap.natoms):
           if not snap.aselect[i]: continue
-          exec ccmd
+          ldict = {'snap':snap,'i':i}
+          exec(ccmd,globals(),ldict)
+          flag = ldict['flag']
           if not flag:
             snap.aselect[i] = 0
             snap.nselect -= 1
-      for i in xrange(data.nsnaps):
+      for i in range(data.nsnaps):
         if data.snaps[i].tselect:
-          print "%d atoms of %d selected in first step %d" % \
+          print("%d atoms of %d selected in first step %d" % \
-                (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
+                (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
           break
-      for i in xrange(data.nsnaps-1,-1,-1):
+      for i in range(data.nsnaps-1,-1,-1):
         if data.snaps[i].tselect:
-          print "%d atoms of %d selected in last step %d" % \
+          print("%d atoms of %d selected in last step %d" % \
-                (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
+                (data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
           break
 
     else:                                        # one timestep
       n = data.findtime(args[0])
       snap = data.snaps[n]
-      for i in xrange(snap.natoms):
+      for i in range(snap.natoms):
         if not snap.aselect[i]: continue
-        exec ccmd
+        ldict = {'snap':snap,'i':i}
+        exec(ccmd,globals(),ldict)
+        flag = ldict['flag']
         if not flag:
           snap.aselect[i] = 0
           snap.nselect -= 1

src/dump2force.py

@@ -27,6 +27,7 @@ and dump match the format here - this will be checked in future!
 
 """
 
+from __future__ import print_function, absolute_import
 from evtk.vtk import VtkFile, VtkGroup, VtkUnstructuredGrid
 from bdump import bdump
 import numpy as np
@@ -80,7 +81,7 @@ timestep = forcedata.next()
 # NOTE: the first timesteps are often blank, and then natoms returns 0, so this doesn't really work...
 #
 if forcedata.snaps[fileindex].natoms !=0 and len(forcedata.snaps[0].atoms[0]) < 12:
-    print "Error - dump file requires at least all parameters from a compute pair/gran/local id pos force (12 in total)"
+    print("Error - dump file requires at least all parameters from a compute pair/gran/local id pos force (12 in total)")
     sys.exit()
 
 # loop through available timesteps
@@ -104,7 +105,7 @@ while timestep >= 0:
     if forcedata.snaps[fileindex].natoms == 0:
         vtufile = fileprefix+'_'+str(timestep)+'.vtu'
         vtufile = os.path.join(outputdir,vtufile)
-        vtuwrite = file(vtufile,'w')
+        vtuwrite = open(vtufile,'w')
         vtuwrite.write("""<?xml version="1.0"?>
 <VTKFile byte_order="LittleEndian" version="0.1" type="UnstructuredGrid">
 <UnstructuredGrid>
@@ -134,8 +135,8 @@ while timestep >= 0:
         nconnex = ncells - nperiodic
 
         # extract the IDs as an array of integers
-        id1 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id1"]],dtype=long)
+        id1 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id1"]],dtype=int)
-        id2 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id2"]],dtype=long)
+        id2 = np.array(forcedata.snaps[fileindex].atoms[:,forcedata.names["id2"]],dtype=int)
 
         # and convert to lists
         id1 = id1.tolist()
@@ -153,7 +154,7 @@ while timestep >= 0:
         # number of points = number of unique IDs (particles)
         npoints = len(ids)
 
-        print 'Timestep:',str(timestep),'npoints=',str(npoints),'ncells=',str(ncells),'nperiodic=',nperiodic, 'nconnex=',str(nconnex)
+        print('Timestep:',str(timestep),'npoints=',str(npoints),'ncells=',str(ncells),'nperiodic=',nperiodic, 'nconnex=',str(nconnex))
 
 
         # ******************************************

src/ensight.py

@@ -8,10 +8,15 @@
 
 # ensight tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, types
+
 oneline = "Convert LAMMPS snapshots or meshes to Ensight format"
 
 docstr = """
-e = ensight(d)	     d = object with atoms or elements (dump,data,mdump)
+e = ensight(d)       d = object with atoms or elements (dump,data,mdump)
 e.change = 1         set to 1 if element nodal xyz change with time (def = 0)
 e.maxtype = 10       max particle type, set if query to data will be bad
 
@@ -50,10 +55,6 @@ e.single(N)          same args as one() prepended by N, but write a single snap
 #   which = 0 for particles, 1 for elements
 #   change = 0 for unchanging mesh coords, 1 for changing mesh coords (def = 0)
 
-# Imports and external programs
-
-import sys, types
-
 # Class definition
 
 class ensight:
@@ -64,16 +65,16 @@ class ensight:
     self.change = 0
     self.maxtype = 0
     self.data = data
-    if type(data) is types.InstanceType and ".dump" in str(data.__class__):
+    if isinstance(data, object) and ".dump" in str(data.__class__):
       self.which = 0
-    elif type(data) is types.InstanceType and ".data" in str(data.__class__):
+    elif isinstance(data, object) and ".data" in str(data.__class__):
       self.which = 0
-    elif type(data) is types.InstanceType and ".mdump" in str(data.__class__):
+    elif isinstance(data, object) and ".mdump" in str(data.__class__):
       self.which = 1
-    elif type(data) is types.InstanceType and ".cdata" in str(data.__class__):
+    elif isinstance(data, object) and ".cdata" in str(data.__class__):
       self.which = 1
     else:
-      raise StandardError,"unrecognized object passed to ensight"
+      raise Exception("unrecognized object passed to ensight")
 
   # --------------------------------------------------------------------
 
@@ -114,34 +115,34 @@ class ensight:
       if flag == -1: break
 
       if self.which == 0:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,atoms,bonds,tris,lines = self.data.viz(which)
         self.coord_file_atoms(f,box,atoms)
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
       elif self.change == 0 and first:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
         self.coord_file_elements(f,box,nodes,elements)
         etype = len(elements[0])
         first = 0
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
       elif self.change:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
         self.coord_file_elements(f,box,nodes,elements)
         etype = len(elements[0])
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
 
       for i in range(len(pairs)):
-        print >>vfiles[i],"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=vfiles[i])
         values = self.data.vecs(time,pairs[i][0])
         if self.which == 0:
           self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values)
         else:
           self.variable_file_elements(vfiles[i],pairs[i][1],etype,values)
-        print >>vfiles[i],"END TIME STEP"
+        print("END TIME STEP", file=vfiles[i])
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
@@ -150,7 +151,7 @@ class ensight:
     f.close()
     for f in vfiles: f.close()
 
-    print "\nwrote %s snapshots in Ensight format" % n
+    print("\nwrote %s snapshots in Ensight format" % n)
 
   # --------------------------------------------------------------------
 
@@ -181,41 +182,41 @@ class ensight:
     first = 1
     n = etype = 0
     while 1:
-      time = self.data.next()
+      time = next(self.data)
       if time == -1: break
       times.append(time)
       self.data.tselect.one(time)
       self.data.delete()
 
       if self.which == 0:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,atoms,bonds,tris,lines = self.data.viz(0)
         self.coord_file_atoms(f,box,atoms)
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
       elif self.change == 0 and first:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,nodes,elements,nvalues,evalues = self.data.mviz(0)
         self.coord_file_elements(f,box,nodes,elements)
         etype = len(elements[0])
         first = 0
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
       elif self.change:
-        print >>f,"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=f)
         time,box,nodes,elements,nvalues,evalues = self.data.mviz(0)
         self.coord_file_elements(f,box,nodes,elements)
         etype = len(elements[0])
-        print >>f,"END TIME STEP"
+        print("END TIME STEP", file=f)
 
       for i in range(len(pairs)):
-        print >>vfiles[i],"BEGIN TIME STEP"
+        print("BEGIN TIME STEP", file=vfiles[i])
         values = self.data.vecs(time,pairs[i][0])
         if self.which == 0:
           self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values)
         else:
           self.variable_file_elements(vfiles[i],pairs[i][1],etype,values)
-        print >>vfiles[i],"END TIME STEP"
+        print("END TIME STEP", file=vfiles[i])
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
@@ -230,7 +231,7 @@ class ensight:
     self.case_file(f,root,pairs,0,len(times),times)
     f.close()
 
-    print "\nwrote %s snapshots in Ensight format" % n
+    print("\nwrote %s snapshots in Ensight format" % n)
 
   # --------------------------------------------------------------------
 
@@ -268,20 +269,20 @@ class ensight:
       files = []
       if n < 10:
         file = root + "000" + str(n) + ".xyz"
-	for pair in pairs:
+        for pair in pairs:
-	  files.append(root + "000" + str(n) + "." + pair[0])
+          files.append(root + "000" + str(n) + "." + pair[0])
       elif n < 100:
         file = root + "00" + str(n) + ".xyz"
-	for pair in pairs:
+        for pair in pairs:
-	  files.append(root + "00" + str(n) + "." + pair[0])
+          files.append(root + "00" + str(n) + "." + pair[0])
       elif n < 1000:
         file = root + "0" + str(n) + ".xyz"
-	for pair in pairs:
+        for pair in pairs:
-	  files.append(root + "0" + str(n) + "." + pair[0])
+          files.append(root + "0" + str(n) + "." + pair[0])
       else:
         file = root + str(n) + ".xyz"
-	for pair in pairs:
+        for pair in pairs:
-	  files.append(root + str(n) + "." + pair[0])
+          files.append(root + str(n) + "." + pair[0])
 
       if self.which == 0:
         f = open(file,"w")
@@ -309,13 +310,13 @@ class ensight:
           self.variable_file_atoms(f,pairs[i][1],atoms,values)
         else:
           self.variable_file_elements(f,pairs[i][1],etype,values)
-	f.close()
+        f.close()
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
-    print "\nwrote %s snapshots in Ensight format" % n
+    print("\nwrote %s snapshots in Ensight format" % n)
 
   # --------------------------------------------------------------------
 
@@ -367,55 +368,55 @@ class ensight:
   # write Ensight case file
 
   def case_file(self,f,root,pairs,multifile,nsnaps,times):
-    print >>f,"# Ensight case file\n"
+    print("# Ensight case file\n", file=f)
-    print >>f,"FORMAT\ntype: ensight gold\n"
+    print("FORMAT\ntype: ensight gold\n", file=f)
 
     if self.which == 0:
       if multifile:
 #        print >>f,"GEOMETRY\nmodel: %s****.xyz change_coords_only\n" % root
-        print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root
+        print("GEOMETRY\nmodel: %s****.xyz\n" % root, file=f)
       else:
 #        print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz change_coords_only\n" % root
-        print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root
+        print("GEOMETRY\nmodel: 1 1 %s.xyz\n" % root, file=f)
     else:
       if self.change == 0:
-        print >>f,"GEOMETRY\nmodel: %s.xyz\n" % root
+        print("GEOMETRY\nmodel: %s.xyz\n" % root, file=f)
       elif multifile:
-        print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root
+        print("GEOMETRY\nmodel: %s****.xyz\n" % root, file=f)
       else:
-        print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root
+        print("GEOMETRY\nmodel: 1 1 %s.xyz\n" % root, file=f)
 
     if len(pairs):
-      print >>f,"VARIABLE"
+      print("VARIABLE", file=f)
       for pair in pairs:
         if self.which == 0:
           if multifile:
-            print >>f,"scalar per node: %s %s****.%s" % (pair[1],root,pair[0])
+            print("scalar per node: %s %s****.%s" % (pair[1],root,pair[0]), file=f)
           else:
-            print >>f,"scalar per node: 1 1 %s %s.%s" % (pair[1],root,pair[0])
+            print("scalar per node: 1 1 %s %s.%s" % (pair[1],root,pair[0]), file=f)
         else:
           if multifile:
-            print >>f,"scalar per element: %s %s****.%s" % (pair[1],root,pair[0])
+            print("scalar per element: %s %s****.%s" % (pair[1],root,pair[0]), file=f)
           else:
-            print >>f,"scalar per element: 1 1 %s %s.%s" % (pair[1],root,pair[0])
+            print("scalar per element: 1 1 %s %s.%s" % (pair[1],root,pair[0]), file=f)
-      print >>f
+      print(file=f)
 
-    print >>f,"TIME"
+    print("TIME", file=f)
-    print >>f,"time set: 1"
+    print("time set: 1", file=f)
-    print >>f,"number of steps:",nsnaps
+    print("number of steps:",nsnaps, file=f)
-    print >>f,"filename start number: 0"
+    print("filename start number: 0", file=f)
-    print >>f,"filename increment: 1"
+    print("filename increment: 1", file=f)
-    print >>f,"time values:"
+    print("time values:", file=f)
     for i in range(nsnaps):
-      print >>f,times[i],
+      print(times[i], end=' ', file=f)
-      if i % 10 == 9: print >>f
+      if i % 10 == 9: print(file=f)
-    print >>f
+    print(file=f)
-    print >>f
+    print(file=f)
 
     if not multifile:
-      print >>f,"FILE"
+      print("FILE", file=f)
-      print >>f,"file set: 1"
+      print("file set: 1", file=f)
-      print >>f,"number of steps:",nsnaps
+      print("number of steps:",nsnaps, file=f)
 
   # --------------------------------------------------------------------
   # write Ensight coordinates for atoms
@@ -423,65 +424,65 @@ class ensight:
   # one part = coords for all atoms of a single type
 
   def coord_file_atoms(self,f,box,atoms):
-    print >>f,"Particle geometry\nfor a collection of atoms"
+    print("Particle geometry\nfor a collection of atoms", file=f)
-    print >>f,"node id given"
+    print("node id given", file=f)
-    print >>f,"element id off"
+    print("element id off", file=f)
-    print >>f,"extents"
+    print("extents", file=f)
-    print >>f,"%12.5e%12.5e" % (box[0],box[3])
+    print("%12.5e%12.5e" % (box[0],box[3]), file=f)
-    print >>f,"%12.5e%12.5e" % (box[1],box[4])
+    print("%12.5e%12.5e" % (box[1],box[4]), file=f)
-    print >>f,"%12.5e%12.5e" % (box[2],box[5])
+    print("%12.5e%12.5e" % (box[2],box[5]), file=f)
 
-    for type in xrange(1,self.maxtype+1):
+    for type in range(1,self.maxtype+1):
-      print >>f,"part"
+      print("part", file=f)
-      print >>f,"%10d" % type
+      print("%10d" % type, file=f)
-      print >>f,"type",type
+      print("type",type, file=f)
-      print >>f,"coordinates"
+      print("coordinates", file=f)
       group = [atom for atom in atoms if int(atom[1]) == type]
-      print >>f,"%10d" % len(group)
+      print("%10d" % len(group), file=f)
-      for atom in group: print >>f,"%10d" % int(atom[0])
+      for atom in group: print("%10d" % int(atom[0]), file=f)
-      for atom in group: print >>f,"%12.5e" % atom[2]
+      for atom in group: print("%12.5e" % atom[2], file=f)
-      for atom in group: print >>f,"%12.5e" % atom[3]
+      for atom in group: print("%12.5e" % atom[3], file=f)
-      for atom in group: print >>f,"%12.5e" % atom[4]
+      for atom in group: print("%12.5e" % atom[4], file=f)
-      print >>f,"point"
+      print("point", file=f)
-      print >>f,"%10d" % len(group)
+      print("%10d" % len(group), file=f)
-      for i in xrange(1,len(group)+1): print >>f,"%10d" % i
+      for i in range(1,len(group)+1): print("%10d" % i, file=f)
 
   # --------------------------------------------------------------------
   # write Ensight coordinates for elements
 
   def coord_file_elements(self,f,box,nodes,elements):
-    print >>f,"Element geometry\nfor a collection of elements"
+    print("Element geometry\nfor a collection of elements", file=f)
-    print >>f,"node id given"
+    print("node id given", file=f)
-    print >>f,"element id given"
+    print("element id given", file=f)
-    print >>f,"extents"
+    print("extents", file=f)
-    print >>f,"%12.5e%12.5e" % (box[0],box[3])
+    print("%12.5e%12.5e" % (box[0],box[3]), file=f)
-    print >>f,"%12.5e%12.5e" % (box[1],box[4])
+    print("%12.5e%12.5e" % (box[1],box[4]), file=f)
-    print >>f,"%12.5e%12.5e" % (box[2],box[5])
+    print("%12.5e%12.5e" % (box[2],box[5]), file=f)
 
-    print >>f,"part"
+    print("part", file=f)
-    print >>f,"%10d" % 1
+    print("%10d" % 1, file=f)
-    print >>f,"all elements"
+    print("all elements", file=f)
-    print >>f,"coordinates"
+    print("coordinates", file=f)
-    print >>f,"%10d" % len(nodes)
+    print("%10d" % len(nodes), file=f)
-    for node in nodes: print >>f,"%10d" % int(node[0])
+    for node in nodes: print("%10d" % int(node[0]), file=f)
-    for node in nodes: print >>f,"%12.5e" % node[2]
+    for node in nodes: print("%12.5e" % node[2], file=f)
-    for node in nodes: print >>f,"%12.5e" % node[3]
+    for node in nodes: print("%12.5e" % node[3], file=f)
-    for node in nodes: print >>f,"%12.5e" % node[4]
+    for node in nodes: print("%12.5e" % node[4], file=f)
 
-    if len(elements[0]) == 5: print >>f,"tria3"
+    if len(elements[0]) == 5: print("tria3", file=f)
-    elif len(elements[0]) == 6: print >>f,"tetra4"
+    elif len(elements[0]) == 6: print("tetra4", file=f)
-    else: raise StandardError,"unrecognized element type"
+    else: raise Exception("unrecognized element type")
-    print >>f,"%10d" % len(elements)
+    print("%10d" % len(elements), file=f)
 
-    for element in elements: print >>f,"%10d" % int(element[0])
+    for element in elements: print("%10d" % int(element[0]), file=f)
     if len(elements[0]) == 5:
       for element in elements:
-        print >>f,"%10d%10d%10d" % \
+        print("%10d%10d%10d" % \
-              (int(element[2]),int(element[3]),int(element[4]))
+              (int(element[2]),int(element[3]),int(element[4])), file=f)
     elif len(elements[0]) == 6:
       for element in elements:
-        print >>f,"%10d%10d%10d%10d" % \
+        print("%10d%10d%10d%10d" % \
-              (int(element[2]),int(element[3]),int(element[4]),int(element[5]))
+              (int(element[2]),int(element[3]),int(element[4]),int(element[5])), file=f)
 
   # --------------------------------------------------------------------
   # write Ensight variable values for atoms
@@ -489,22 +490,22 @@ class ensight:
   # one part = values for all atoms of a single type
 
   def variable_file_atoms(self,f,name,atoms,values):
-    print >>f,"Particle %s" % name
+    print("Particle %s" % name, file=f)
-    for type in xrange(1,self.maxtype+1):
+    for type in range(1,self.maxtype+1):
-      print >>f,"part"
+      print("part", file=f)
-      print >>f,"%10d" % type
+      print("%10d" % type, file=f)
-      print >>f,"coordinates"
+      print("coordinates", file=f)
-      group = [values[i] for i in xrange(len(atoms))
+      group = [values[i] for i in range(len(atoms))
                if int(atoms[i][1]) == type]
-      for value in group: print >>f,"%12.5e" % value
+      for value in group: print("%12.5e" % value, file=f)
 
   # --------------------------------------------------------------------
   # write Ensight variable values for elements
 
   def variable_file_elements(self,f,name,etype,values):
-    print >>f,"Element %s" % name
+    print("Element %s" % name, file=f)
-    print >>f,"part"
+    print("part", file=f)
-    print >>f,"%10d" % 1
+    print("%10d" % 1, file=f)
-    if etype == 5: print >>f,"tria3"
+    if etype == 5: print("tria3", file=f)
-    elif etype == 6: print >>f,"tetra4"
+    elif etype == 6: print("tetra4", file=f)
-    for value in values: print >>f,"%12.5e" % value
+    for value in values: print("%12.5e" % value, file=f)

src/gl.py

@@ -8,6 +8,16 @@
 
 # gl tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+
+from math import sin,cos,sqrt,pi,acos
+from OpenGL.Tk import *
+from OpenGL.GLUT import *
+from PIL import Image
+from vizinfo import vizinfo
+
 oneline = "3d interactive visualization via OpenGL"
 
 docstr = """
@@ -16,8 +26,8 @@ g = gl(d)                   create OpenGL display for data in d
   d = atom snapshot object (dump, data)
 
 g.bg("black")               set background color (def = "black")
-g.size(N)		    set image size to NxN
+g.size(N)                   set image size to NxN
-g.size(N,M)		    set image size to NxM
+g.size(N,M)                 set image size to NxM
 g.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
 g.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
 g.zoom(0.5)                 scale image by factor (def = 1)
@@ -43,9 +53,9 @@ g.select = ""               no extra aselect (default)
 
   %g varies from 0.0 to 1.0 from beginning to end of all()
 
-g.acol(2,"green")		   set atom colors by atom type (1-N)
+g.acol(2,"green")                  set atom colors by atom type (1-N)
-g.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+g.acol([2,4],["red","blue"])       1st arg = one type or list of types
-g.acol(0,"blue")	           2nd arg = one color or list of colors
+g.acol(0,"blue")                   2nd arg = one color or list of colors
 g.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
 g.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
@@ -55,19 +65,19 @@ g.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
 g.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol()
 
-g.bcol()			   set bond color, same args as acol()
+g.bcol()                           set bond color, same args as acol()
-g.brad()			   set bond thickness, same args as arad()
+g.brad()                           set bond thickness, same args as arad()
 
-g.tcol()			   set triangle color, same args as acol()
+g.tcol()                           set triangle color, same args as acol()
-g.tfill()			   set triangle fill, 0 fill, 1 line, 2 both
+g.tfill()                          set triangle fill, 0 fill, 1 line, 2 both
 
 g.lcol()                           set line color, same args as acol()
 g.lrad()                           set line thickness, same args as arad()
 
 g.adef()                           set atom/bond/tri/line properties to default
-g.bdef()			   default = "loop" for colors, 0.45 for radii
+g.bdef()                           default = "loop" for colors, 0.45 for radii
-g.tdef()  			   default = 0.25 for bond/line thickness
+g.tdef()                           default = 0.25 for bond/line thickness
-g.ldef()  			   default = 0 fill
+g.ldef()                           default = 0 fill
 
   by default 100 types are assigned
   if atom/bond/tri/line has type > # defined properties, is an error
@@ -122,14 +132,6 @@ g.sview(theta,phi,x,y,scale,up)      set all view parameters
 #   up[3] = screen up direction in simulation box (unit vector)
 #   right[3] = screen right direction in simulation box (unit vector)
 
-# Imports and external programs
-
-from math import sin,cos,sqrt,pi,acos
-from OpenGL.Tk import *
-from OpenGL.GLUT import *
-import Image
-from vizinfo import vizinfo
-
 # Class definition
 
 class gl:
@@ -312,7 +314,7 @@ class gl:
       self.up[1] = sin(pi*self.azphi/180)
       self.up[2] = 0.0
     else:
-      dot = self.view[2]		   # dot = (0,0,1) . view
+      dot = self.view[2]                   # dot = (0,0,1) . view
       self.up[0] = -dot*self.view[0]       # up projected onto v = dot * v
       self.up[1] = -dot*self.view[1]       # up perp to v = up - dot * v
       self.up[2] = 1.0 - dot*self.view[2]
@@ -442,8 +444,8 @@ class gl:
   # --------------------------------------------------------------------
 
   def shift(self,x,y):
-    self.xshift = x;
+    self.xshift = x
-    self.yshift = y;
+    self.yshift = y
     self.setview()
     self.w.tkRedraw()
 
@@ -500,7 +502,7 @@ class gl:
   # add GL-specific info to each bond
 
   def reload(self):
-    print "Loading data into gl tool ..."
+    print("Loading data into gl tool ...")
     data = self.data
 
     self.timeframes = []
@@ -528,9 +530,9 @@ class gl:
       self.triframes.append(tris)
       self.lineframes.append(lines)
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
-    print
+    print()
 
     self.nframes = len(self.timeframes)
     self.distance = compute_distance(self.boxframes[0])
@@ -636,7 +638,7 @@ class gl:
                           fraction*(self.scale_stop - self.scale_start)
           self.viewupright()
 
-	if n == nstart or self.panflag: self.center = compute_center(box)
+        if n == nstart or self.panflag: self.center = compute_center(box)
 
         if bonds: self.bonds_augment(bonds)
 
@@ -652,7 +654,7 @@ class gl:
         self.w.tkRedraw()
         self.save(file)
 
-        print time,
+        print(time, end=' ')
         sys.stdout.flush()
         i += 1
         n += 1
@@ -691,7 +693,7 @@ class gl:
                           fraction*(self.scale_stop - self.scale_start)
           self.viewupright()
 
-	if n == nstart or self.panflag: self.center = compute_center(box)
+        if n == nstart or self.panflag: self.center = compute_center(box)
 
         if bonds: self.bonds_augment(bonds)
 
@@ -707,11 +709,11 @@ class gl:
         self.w.tkRedraw()
         self.save(file)
 
-        print n,
+        print(n, end=' ')
         sys.stdout.flush()
         n += 1
 
-    print "\n%d images" % ncount
+    print("\n%d images" % ncount)
 
   # --------------------------------------------------------------------
 
@@ -777,11 +779,11 @@ class gl:
       ncolor = self.vizinfo.nlcolor
       for line in self.linedraw:
         itype = int(line[1])
-        if itype > ncolor: raise StandardError,"line type too big"
+        if itype > ncolor: raise Exception("line type too big")
         red,green,blue = self.vizinfo.lcolor[itype]
         glColor3f(red,green,blue)
         thick = self.vizinfo.lrad[itype]
-	glLineWidth(thick)
+        glLineWidth(thick)
         glBegin(GL_LINES)
         glVertex3f(line[2],line[3],line[4])
         glVertex3f(line[5],line[6],line[7])
@@ -826,7 +828,7 @@ class gl:
           for bond in self.bonddraw:
             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()
@@ -849,7 +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);
@@ -907,7 +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()
@@ -939,7 +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]);
@@ -991,7 +993,7 @@ class gl:
 
     # create new calllist for each atom type
 
-    for itype in xrange(1,self.vizinfo.nacolor+1):
+    for itype in range(1,self.vizinfo.nacolor+1):
       if self.calllist[itype]: glDeleteLists(self.calllist[itype],1)
       ilist = glGenLists(1)
       self.calllist[itype] = ilist
@@ -1101,7 +1103,8 @@ class gl:
 
     pstring = glReadPixels(0,0,self.xpixels,self.ypixels,
                            GL_RGBA,GL_UNSIGNED_BYTE)
-    snapshot = Image.fromstring("RGBA",(self.xpixels,self.ypixels),pstring)
+    #snapshot = Image.fromstring("RGBA",(self.xpixels,self.ypixels),pstring)
+    snapshot = Image.frombytes("RGBA",(self.xpixels,self.ypixels),pstring)
     snapshot = snapshot.transpose(Image.FLIP_TOP_BOTTOM)
 
     if not file: file = self.file
@@ -1110,8 +1113,11 @@ class gl:
   # --------------------------------------------------------------------
 
   def adef(self):
-    self.vizinfo.setcolors("atom",range(100),"loop")
+    rlist = list(range(100))
-    self.vizinfo.setradii("atom",range(100),0.45)
+    #self.vizinfo.setcolors("atom",list(range(100)),"loop")
+    #self.vizinfo.setradii("atom",list(range(100)),0.45)
+    self.vizinfo.setcolors("atom",rlist,"loop")
+    self.vizinfo.setradii("atom",rlist,0.45)
     self.make_atom_calllist()
     self.cachelist = -self.cachelist
     self.w.tkRedraw()
@@ -1119,24 +1125,24 @@ class gl:
   # --------------------------------------------------------------------
 
   def bdef(self):
-    self.vizinfo.setcolors("bond",range(100),"loop")
+    self.vizinfo.setcolors("bond",list(range(100)),"loop")
-    self.vizinfo.setradii("bond",range(100),0.25)
+    self.vizinfo.setradii("bond",list(range(100)),0.25)
     self.cachelist = -self.cachelist
     self.w.tkRedraw()
 
   # --------------------------------------------------------------------
 
   def tdef(self):
-    self.vizinfo.setcolors("tri",range(100),"loop")
+    self.vizinfo.setcolors("tri",list(range(100)),"loop")
-    self.vizinfo.setfills("tri",range(100),0)  
+    self.vizinfo.setfills("tri",list(range(100)),0)
     self.cachelist = -self.cachelist
     self.w.tkRedraw()
 
   # --------------------------------------------------------------------
 
   def ldef(self):
-    self.vizinfo.setcolors("line",range(100),"loop")  
+    self.vizinfo.setcolors("line",list(range(100)),"loop")
-    self.vizinfo.setradii("line",range(100),0.25)
+    self.vizinfo.setradii("line",list(range(100)),0.25)
     self.cachelist = -self.cachelist
     self.w.tkRedraw()
 

src/gnu.py

@@ -8,15 +8,20 @@
 
 # gnu tool
 
+# Imports and external programs
+
+from __future__ import print_function, division, absolute_import
+import types, os
+
 oneline = "Create plots via GnuPlot plotting program"
 
 docstr = """
-g = gnu()		       start up GnuPlot
+g = gnu()                      start up GnuPlot
-g.stop()		       shut down GnuPlot process
+g.stop()                       shut down GnuPlot process
 
 g.plot(a)                      plot vector A against linear index
-g.plot(a,b)	 	       plot B against A
+g.plot(a,b)                    plot B against A
-g.plot(a,b,c,d,...)	       plot B against A, D against C, etc
+g.plot(a,b,c,d,...)            plot B against A, D against C, etc
 g.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
   each plot argument can be a tuple, list, or Numeric/NumPy vector
@@ -29,21 +34,21 @@ g.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
 g("plot 'file.dat' using 2:3 with lines")      execute string in GnuPlot
 
-g.enter()	   	                enter GnuPlot shell
+g.enter()                               enter GnuPlot shell
 gnuplot> plot sin(x) with lines         type commands directly to GnuPlot
-gnuplot> exit, quit	      	        exit GnuPlot shell
+gnuplot> exit, quit                     exit GnuPlot shell
 
 g.export("data",range(100),a,...)       create file with columns of numbers
 
   all vectors must be of equal length
   could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
 
-g.select(N)  	               figure N becomes the current plot
+g.select(N)                    figure N becomes the current plot
 
   subsequent commands apply to this plot
 
-g.hide(N)  	               delete window for figure N
+g.hide(N)                      delete window for figure N
-g.save("file")	               save current plot as file.eps
+g.save("file")                 save current plot as file.eps
 
 Set attributes for current plot:
 
@@ -82,10 +87,6 @@ g.curve(N,'r')                 set color of curve N
 #   figures = list of figure objects with each plot's attributes
 #             so they aren't lost between replots
 
-# Imports and external programs
-
-import types, os
-
 try: from DEFAULTS import PIZZA_GNUPLOT
 except: PIZZA_GNUPLOT = "gnuplot"
 try: from DEFAULTS import PIZZA_GNUTERM
@@ -119,7 +120,7 @@ class gnu:
 
   def enter(self):
     while 1:
-      command = raw_input("gnuplot> ")
+      command = input("gnuplot> ")
       if command == "quit" or command == "exit": return
       self.__call__(command)
 
@@ -129,15 +130,15 @@ class gnu:
   def plot(self,*vectors):
     if len(vectors) == 1:
       file = self.file + ".%d.1" % self.current
-      linear = range(len(vectors[0]))
+      linear = list(range(len(vectors[0])))
       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)
+        file = self.file + ".%d.%d" % (self.current,i//2+1)
         self.export(file,vectors[i],vectors[i+1])
-      self.figures[self.current-1].ncurves = len(vectors)/2
+      self.figures[self.current-1].ncurves = len(vectors)//2
     self.draw()
 
   # --------------------------------------------------------------------
@@ -167,13 +168,13 @@ 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(vectors[j][i], end=' ', file=f)
-      print >>f
+      print(file=f)
     f.close()
 
   # --------------------------------------------------------------------
@@ -353,7 +354,7 @@ class gnu:
     for i in range(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]
+        cmd += "'" + file + "' using 1:2 with lines lc %d, " % fig.colors[i]
       else:
         cmd += "'" + file + "' using 1:2 with lines, "
     self.__call__(cmd[:-2])

src/histo.py

@@ -43,7 +43,7 @@ class histo:
     if dim == 'x': idim = 2
     elif dim == 'y': idim = 3
     elif dim == 'z': idim = 4
-    else: raise StandardError,"illegal dim value"
+    else: raise Exception("illegal dim value")
 
     y = nbins*[0]
 
@@ -78,9 +78,9 @@ class histo:
       n += 1
 
     x = nbins*[0]
-    for i in xrange(nbins): x[i] = (i+0.5)*delta
+    for i in range(nbins): x[i] = (i+0.5)*delta
 
-    print "histogram snapshots = ",n
+    print("histogram snapshots = ",n)
-    print "histogram counts (per snap) = %d (%g)" % (count,float(count)/n)
+    print("histogram counts (per snap) = %d (%g)" % (count,float(count)/n))
-    print "histogram bounds = ",lo,hi
+    print("histogram bounds = ",lo,hi)
     return x,y

src/image.py

@@ -8,19 +8,35 @@
 
 # image tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, os, re, glob
+try:
+  import commands
+except ImportError:
+  import subprocess as commands
+from math import *
+try:
+  from Tkinter import *
+except ImportError:
+  from tkinter import *
+import Pmw
+from PIL import Image
+
 oneline = "View and manipulate images"
 
 docstr = """
 i = image("my1.gif my2.gif")    display thumbnails of matching images
 i = image("*.png *.gif")        wildcards allowed
-i = image("")	   		blank string matches all image suffixes
+i = image("")                   blank string matches all image suffixes
-i = image()			no display window opened if no arg
+i = image()                     no display window opened if no arg
 
   image suffixes for blank string = *.png, *.bmp, *.gif, *.tiff, *.tif
   click on a thumbnail to view it full-size
   click on thumbnail again to remove full-sized version
 
-i.view("*.png *.gif")	        display thumbnails of matching images
+i.view("*.png *.gif")           display thumbnails of matching images
 
   view arg is same as constructor arg
 
@@ -46,14 +62,6 @@ i.montage("-geometry 512x512","i*.png","new.png")       1st arg is switch
 
 # Variables
 
-# Imports and external programs
-
-import sys, os, commands, re, glob
-from math import *
-from Tkinter import *
-import Pmw
-import Image,ImageTk
-
 try: from DEFAULTS import PIZZA_CONVERT
 except: PIZZA_CONVERT = "convert"
 try: from DEFAULTS import PIZZA_MONTAGE
@@ -77,7 +85,7 @@ class image:
     list = str.split(filestr)
     files = []
     for file in list: files += glob.glob(file)
-    if len(files) == 0: raise StandardError, "no image files to load"
+    if len(files) == 0: raise Exception("no image files to load")
 
     # grab Tk instance from main
 
@@ -93,7 +101,7 @@ class image:
     pane = scroll.interior()
 
     ncolumns = 4
-    for i in xrange(len(files)):
+    for i in range(len(files)):
 
       # create new row frame if 1st in column
 
@@ -107,7 +115,7 @@ class image:
       imt.thumbnail((60,60),Image.ANTIALIAS)
       basename = os.path.basename(files[i])
       imt.save("tmp." + basename)
-      thumbnail = ImageTk.PhotoImage(file = "tmp." + basename)
+      thumbnail = PhotoImage(file = "tmp." + basename)
       os.remove("tmp." + basename)
 
       # read in full size image
@@ -115,7 +123,7 @@ class image:
       # create button that calls the thumbnail, label with filename
       # buttton needs to store thumbnail else it is garbage collected
 
-      big = ImageTk.PhotoImage(file=files[i])
+      big = PhotoImage(file=files[i])
       obj = thumbnails(gui,files[i],big,thumbnail)
       Button(oneframe,image=thumbnail,command=obj.display).pack(side=TOP)
       Label(oneframe,text=basename).pack(side=BOTTOM)
@@ -150,17 +158,17 @@ class image:
       middle = re.search(expr,file1).group(1)
       file2 = "%s%s%s" % (pre2,middle,post2)
       cmd = "%s %s %s %s" % (PIZZA_CONVERT,switch,file1,file2)
-      print middle,
+      print(middle, end=' ')
       sys.stdout.flush()
       commands.getoutput(cmd)
-    print
+    print()
 
   # --------------------------------------------------------------------
   # wrapper on ImageMagick montage command
 
   def montage(self,switch,*fileargs):
     nsets = len(fileargs)
-    if nsets < 2: raise StandardError,"montage requires 2 or more file args"
+    if nsets < 2: raise Exception("montage requires 2 or more file args")
 
     for i in range(nsets):
       if fileargs[i].find('*') < 0:
@@ -174,7 +182,7 @@ class image:
     for i in range(nsets-1):
       filesets.append(glob.glob(fileargs[i]))
       if len(filesets[-1]) != nfiles:
-        raise StandardError,"each montage arg must represent equal # of files"
+        raise Exception("each montage arg must represent equal # of files")
 
     index = fileargs[0].index('*')
     pre1 = fileargs[0][:index]
@@ -191,9 +199,9 @@ class image:
       fileN = "%s%s%s" % (preN,middle,postN)
       cmd += " %s" % fileN
       commands.getoutput(cmd)
-      print middle,
+      print(middle, end=' ')
       sys.stdout.flush()
-    print
+    print()
 
 # --------------------------------------------------------------------
 # thumbnail class
@@ -216,7 +224,7 @@ class thumbnails:
       self.bigexist = 0
       if self.window:
         self.window.destroy()
-	self.window = None
+        self.window = None
 
     # create a new window with the big image
 

src/ldump.py

@@ -8,18 +8,25 @@
 
 # ldump tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, types
+import functools
+from os import popen
+
 oneline = "Read dump files with line segment info"
 
 docstr = """
 l = ldump("dump.one")             read in one or more dump files
-l = ldump("dump.1 dump.2.gz")	  can be gzipped
+l = ldump("dump.1 dump.2.gz")     can be gzipped
-l = ldump("dump.*")		  wildcard expands to multiple files
+l = ldump("dump.*")               wildcard expands to multiple files
-l = ldump("dump.*",0)		  two args = store filenames, but don't read
+l = ldump("dump.*",0)             two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
   no column name assignment is performed
 
-time = l.next()             	  read next snapshot from dump files
+time = l.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -43,7 +50,7 @@ time,box,atoms,bonds,tris,lines = l.viz(index)   return list of viz objects
     lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
       id,type are from associated atom
 
-l.owrap(...)		          wrap lines to same image as their atoms
+l.owrap(...)                      wrap lines to same image as their atoms
 
   owrap() is called by dump tool's owrap()
   useful for wrapping all molecule's atoms/lines the same so it is contiguous
@@ -67,11 +74,6 @@ l.owrap(...)		          wrap lines to same image as their atoms
 #     xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
-# Imports and external programs
-
-import sys, commands, re, glob, types
-from os import popen
-
 try:
     import numpy as np
     oldnumeric = False
@@ -99,7 +101,7 @@ class ldump:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no ldump file specified"
+      raise Exception("no ldump file specified")
 
     if len(list) == 1:
       self.increment = 0
@@ -124,26 +126,26 @@ class ldump:
       snap = self.read_snapshot(f)
       while snap:
         self.snaps.append(snap)
-        print snap.time,
+        print(snap.time, end=' ')
         sys.stdout.flush()
         snap = self.read_snapshot(f)
 
       f.close()
-    print
+    print()
 
     # sort entries by timestep, cull duplicates
 
-    self.snaps.sort(self.compare_time)
+    self.snaps.sort(key = functools.cmp_to_key(self.compare_time))
     self.cull()
     self.nsnaps = len(self.snaps)
-    print "read %d snapshots" % self.nsnaps
+    print("read %d snapshots" % self.nsnaps)
 
   # --------------------------------------------------------------------
   # read next snapshot from list of files
 
   def next(self):
 
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     # read next snapshot in current file using eof as pointer
     # if fail, try next file
@@ -155,15 +157,15 @@ class ldump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
+        self.eof = 0
-	continue
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     self.snaps.append(snap)
@@ -197,14 +199,14 @@ class ldump:
       if snap.natoms:
         words = f.readline().split()
         ncol = len(words)
-        for i in xrange(1,snap.natoms):
+        for i in range(1,snap.natoms):
           words += f.readline().split()
-        floats = map(float,words)
+        floats = list(map(float,words))
         if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
         else: atoms = np.zeros((snap.natoms,ncol),np.float)
         start = 0
         stop = ncol
-        for i in xrange(snap.natoms):
+        for i in range(snap.natoms):
           atoms[i] = floats[start:stop]
           start = stop
           stop += ncol
@@ -219,7 +221,7 @@ class ldump:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "ldump map() requires pairs of mappings"
+      raise Exception("ldump map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -249,9 +251,9 @@ class ldump:
   # --------------------------------------------------------------------
 
   def findtime(self,n):
-    for i in xrange(self.nsnaps):
+    for i in range(self.nsnaps):
       if self.snaps[i].time == n: return i
-    raise StandardError, "no step %d exists" % n
+    raise Exception("no step %d exists" % n)
 
   # --------------------------------------------------------------------
   # delete successive snapshots with duplicate time stamp
@@ -293,7 +295,7 @@ class ldump:
     # don't add line if all 4 values are 0 since not a line
 
     lines = []
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       atom = snap.atoms[i]
       e1x = atom[end1x]
       e1y = atom[end1y]
@@ -323,7 +325,7 @@ class ldump:
     # jdump = atom J in dump's atoms that atom I was owrapped on
     # delx,dely = offset applied to atom I and thus to line I
 
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       tag = atoms[i][id]
       idump = idsdump[tag]
       jdump = idsdump[atomsdump[idump][iother]]

src/log.py

@@ -8,6 +8,13 @@
 
 # log tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob
+import functools
+from os import popen
+
 oneline = "Read LAMMPS log files and extract thermodynamic data"
 
 docstr = """
@@ -28,7 +35,7 @@ nvec = l.nvec                        # of vectors of thermo info
 nlen = l.nlen                        length of each vectors
 names = l.names                      list of vector names
 t,pe,... = l.get("Time","KE",...)    return one or more vectors of values
-l.write("file.txt")	 	     write all vectors to a file
+l.write("file.txt")                  write all vectors to a file
 l.write("file.txt","Time","PE",...)  write listed vectors to a file
 
   get and write allow abbreviated (uniquely) vector names
@@ -50,11 +57,6 @@ l.write("file.txt","Time","PE",...)  write listed vectors to a file
 #   increment = 1 if log file being read incrementally
 #   eof = ptr into incremental file for where to start next read
 
-# Imports and external programs
-
-import sys, re, glob
-from os import popen
-
 try: tmp = PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
 
@@ -76,14 +78,14 @@ class log:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no log file specified"
+      raise Exception("no log file specified")
 
     if len(list) == 1:
       self.increment = 0
       self.read_all()
     else:
       if len(self.flist) > 1:
-        raise StandardError,"can only incrementally read one log file"
+        raise Exception("can only incrementally read one log file")
       self.increment = 1
       self.eof = 0
 
@@ -92,24 +94,24 @@ class log:
 
   def read_all(self):
     self.read_header(self.flist[0])
-    if self.nvec == 0: raise StandardError,"log file has no values"
+    if self.nvec == 0: raise Exception("log file has no values")
 
     # read all files
 
     for file in self.flist: self.read_one(file)
-    print
+    print()
 
     # sort entries by timestep, cull duplicates
 
-    self.data.sort(self.compare)
+    self.data.sort(key = functools.cmp_to_key(self.compare))
     self.cull()
     self.nlen = len(self.data)
-    print "read %d log entries" % self.nlen
+    print("read %d log entries" % self.nlen)
 
   # --------------------------------------------------------------------
 
   def next(self):
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     if self.nvec == 0:
       try: open(self.flist[0],'r')
@@ -124,27 +126,27 @@ class log:
 
   def get(self,*keys):
     if len(keys) == 0:
-      raise StandardError, "no log vectors specified"
+      raise Exception("no log vectors specified")
 
     map = []
     for key in keys:
-      if self.ptr.has_key(key):
+      if key in self.ptr:
         map.append(self.ptr[key])
       else:
         count = 0
         for i in range(self.nvec):
-	  if self.names[i].find(key) == 0:
+          if self.names[i].find(key) == 0:
-	    count += 1
+            count += 1
-	    index = i
+            index = i
         if count == 1:
           map.append(index)
         else:
-          raise StandardError, "unique log vector %s not found" % key
+          raise Exception("unique log vector %s not found" % key)
 
     vecs = []
     for i in range(len(keys)):
       vecs.append(self.nlen * [0])
-      for j in xrange(self.nlen):
+      for j in range(self.nlen):
         vecs[i][j] = self.data[j][map[i]]
 
     if len(keys) == 1: return vecs[0]
@@ -156,26 +158,26 @@ class log:
     if len(keys):
       map = []
       for key in keys:
-        if self.ptr.has_key(key):
+        if key in self.ptr:
           map.append(self.ptr[key])
         else:
           count = 0
           for i in range(self.nvec):
-	    if self.names[i].find(key) == 0:
+            if self.names[i].find(key) == 0:
-	      count += 1
+              count += 1
-	      index = i
+              index = i
           if count == 1:
             map.append(index)
           else:
-            raise StandardError, "unique log vector %s not found" % key
+            raise Exception("unique log vector %s not found" % key)
     else:
-      map = range(self.nvec)
+      map = list(range(self.nvec))
 
     f = open(filename,"w")
-    for i in xrange(self.nlen):
+    for i in range(self.nlen):
-      for j in xrange(len(map)):
+      for j in range(len(map)):
-        print >>f,self.data[i][map[j]],
+        print(self.data[i][map[j]], end=' ', file=f)
-      print >>f
+      print(file=f)
     f.close()
 
   # --------------------------------------------------------------------
@@ -224,7 +226,7 @@ class log:
       keywords.insert(0,"Step")
       i = 0
       for keyword in keywords:
-	self.names.append(keyword)
+        self.names.append(keyword)
         self.ptr[keyword] = i
         i += 1
 
@@ -234,25 +236,25 @@ class log:
       line = txt[s1:s2]
       words = line.split()
       for i in range(len(words)):
-	self.names.append(words[i])
+        self.names.append(words[i])
         self.ptr[words[i]] = i
 
     self.nvec = len(self.names)
 
   # --------------------------------------------------------------------
 
-  def read_one(self,*list):
+  def read_one(self,*flist):
 
     # if 2nd arg exists set file ptr to that value
     # read entire (rest of) file into txt
 
-    file = list[0]
+    file = flist[0]
     if file[-3:] == ".gz":
-      f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb')
+      f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
     else:
-      f = open(file,'rb')
+      f = open(file,'r')
 
-    if len(list) == 2: f.seek(list[1])
+    if len(flist) == 2: f.seek(flist[1])
     txt = f.read()
     if file[-3:] == ".gz": eof = 0
     else: eof = f.tell()
@@ -273,36 +275,36 @@ class log:
 
       if s1 >= 0 and s2 >= 0 and s1 < s2:    # found s1,s2 with s1 before s2
         if self.style == 2:
-	  s1 = txt.find("\n",s1) + 1
+          s1 = txt.find("\n",s1) + 1
       elif s1 >= 0 and s2 >= 0 and s2 < s1:  # found s1,s2 with s2 before s1
         s1 = 0
       elif s1 == -1 and s2 >= 0:             # found s2, but no s1
-	last = 1
+        last = 1
         s1 = 0
       elif s1 >= 0 and s2 == -1:             # found s1, but no s2
         last = 1
         if self.style == 1:
           s2 = txt.rfind("\n--",s1) + 1
         else:
-	  s1 = txt.find("\n",s1) + 1
+          s1 = txt.find("\n",s1) + 1
           s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
+        eof -= len(txt) - s2
       elif s1 == -1 and s2 == -1:            # found neither
                                              # could be end-of-file section
-					     # or entire read was one chunk
+                                             # or entire read was one chunk
 
         if txt.find("Loop time of",start) == start:   # end of file, so exit
-	  eof -= len(txt) - start                     # reset eof to "Loop"
+          eof -= len(txt) - start                     # reset eof to "Loop"
-	  break
+          break
 
-	last = 1                                      # entire read is a chunk
+        last = 1                                      # entire read is a chunk
         s1 = 0
         if self.style == 1:
           s2 = txt.rfind("\n--",s1) + 1
         else:
           s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
+        eof -= len(txt) - s2
-	if s1 == s2: break
+        if s1 == s2: break
 
       chunk = txt[s1:s2-1]
       start = s2
@@ -318,17 +320,17 @@ class log:
           word1 = [re.search(pat1,section).group(1)]
           word2 = re.findall(pat2,section)
           words = word1 + word2
-          self.data.append(map(float,words))
+          self.data.append(list(map(float,words)))
 
       else:
         lines = chunk.split("\n")
         for line in lines:
           words = line.split()
-          self.data.append(map(float,words))
+          self.data.append(list(map(float,words)))
 
       # print last timestep of chunk
 
-      print int(self.data[len(self.data)-1][0]),
+      print(int(self.data[len(self.data)-1][0]), end=' ')
       sys.stdout.flush()
 
     return eof

src/lpp.py

@@ -1,32 +1,33 @@
 #!/usr/bin/env python
 
+from __future__ import print_function, absolute_import
+import getopt
+import os
+import time
+import sys
+import multiprocessing
+import glob
+import vtk
+from math import ceil
+from math import floor
+from dump import dump
 oneline = "writing pp-data in vtk format automatically, saving memory"
 
 docstr = """this is the docstr of LIGGGHTSPostProcessing"""
 
-from dump import dump
-from math import floor
-from math import ceil
-import vtk
-import glob
-import multiprocessing
-import sys
-import time
-import os
-import exceptions
 # changes py p.s. - include a few command line options
-import getopt
+
 
 class lpp:
 
-  #=============================================================================
+  # =============================================================================
   # creates a filelist, seperates it to sublists
   # creates multiple processes
   # calls lppWorker for each sublist
   #   lppWorker
   #   calls dump, vtk and manyGran for the given list of files
   #   returns 0
-  #=============================================================================
+  # =============================================================================
 
   def __init__(self, *list, **kwargs):
     # do argument parsing, raise errors if non-integers were given
@@ -35,43 +36,66 @@ class lpp:
     self.cpunum      = multiprocessing.cpu_count()
     self.chunksize   = 8
     self.overwrite   = True
+    self.Nth         = 1
+    self.timesteps   = "all"
 
     if "--chunksize" in kwargs:
       try:
         if int(kwargs["--chunksize"]) > 0:
           self.chunksize = int(kwargs["--chunksize"])
-        else: raise ValueError
+        else:
+          raise ValueError
       except ValueError:
-        raise ValueError, "Invalid or no argument given for chunksize"
+        raise ValueError("Invalid or no argument given for chunksize")
+
+    if "--Nth" in kwargs:
+      try:
+        if int(kwargs["--Nth"]) > 0 and int(kwargs["--Nth"]) >= self.Nth:
+          self.Nth = int(kwargs["--Nth"])
+        else:
+          raise ValueError
+      except ValueError:
+        raise ValueError("Invalid or no argument given for Nth")
+
+    if "--timesteps" in kwargs:
+      try:
+        self.timesteps = kwargs["--timesteps"]
+      except ValueError:
+        raise ValueError("Invalid or no argument given for timesteps")
 
     if "--cpunum" in kwargs:
       try:
         if int(kwargs["--cpunum"]) > 0 and int(kwargs["--cpunum"]) <= self.cpunum:
           self.cpunum = int(kwargs["--cpunum"])
-        else: raise ValueError
+        else:
+          raise ValueError
       except ValueError:
-        raise ValueError, "Invalid or no argument given for cpunum"
+        raise ValueError("Invalid or no argument given for cpunum")
 
     # do not overwrite existing files
     if "--no-overwrite" in kwargs:
       self.overwrite = False
 
     # suppress output with 'False'
-    if "--debug" in kwargs: self.debugMode = True
+    if "--debug" in kwargs:
-    else: self.debugMode = False
+      self.debugMode = True
+    else:
+      self.debugMode = False
 
     if "--quiet" in kwargs:
       self.output = False
       self.debugMode = False
-    else: self.output = True
+    else:
+      self.output = True
 
     if self.output:
-      print "starting LIGGGHTS memory optimized parallel post processing"
+      print("starting LIGGGHTS memory optimized parallel post processing")
-      print "chunksize:", self.chunksize, "-->",self.chunksize,\
+      print("chunksize:", self.chunksize, "-->",self.chunksize,\
-        "files are processed per chunk. If you run out of memory reduce chunksize."
+        "files are processed per chunk. If you run out of memory reduce chunksize.")
     starttime = time.time()
 
-    if self.debugMode: print "number of process:", os.getpid()
+    if self.debugMode:
+      print("number of process:", os.getpid())
 
     # check whether file-list is nonempty
     self.flist = []
@@ -86,42 +110,47 @@ class lpp:
       self.flist = list[0]
     listlen = len(self.flist)
     if listlen == 0 and len(list) == 1:
-      raise StandardError, "no dump file specified"
+      raise Exception("no dump file specified")
     if listlen == 1 and self.overwrite == False:
-      raise StandardError, "Cannot process single dump files with --no-overwrite."
+      raise Exception("Cannot process single dump files with --no-overwrite.")
 
     if self.output:
-      print "Working with", self.cpunum, "processes..."
+      print("Working with", self.cpunum, "processes...")
 
     # seperate list in pieces+rest
     self.slices = []
 
     residualPresent = int(bool(listlen-floor(listlen/self.chunksize)*self.chunksize))
 
-    for i in xrange(int(floor(listlen/self.chunksize))+residualPresent):
+    for i in range(int(floor(listlen/self.chunksize))+residualPresent):
       slice = self.flist[i*self.chunksize:(i+1)*self.chunksize]
       self.slices.append(slice)
     self.flist = []
 
     output = ""
-    if "-o" in kwargs: output = kwargs["-o"]
+    if "-o" in kwargs:
+      output = kwargs["-o"]
     # generate input for lppWorker
     dumpInput = [{"filelist":self.slices[i],\
       "debugMode":self.debugMode,\
       "output":output,\
-      "overwrite":self.overwrite} \
+      "overwrite":self.overwrite,\
-      for i in xrange(len(self.slices))]
+      "timesteps":self.timesteps,\
+      "Nth":self.Nth} \
+      for i in range(len(self.slices))]
 
-    if self.debugMode: print "dumpInput:",dumpInput
+    if self.debugMode:
+      print("dumpInput:",dumpInput)
 
     numberOfRuns = len(dumpInput)
     i = 0
     while i < len(dumpInput):
 
       if self.output:
-        print "calculating chunks",i+1,"-",min(i+self.cpunum,numberOfRuns),"of",numberOfRuns
+        print("calculating chunks",i+1,"-",min(i+self.cpunum,numberOfRuns),"of",numberOfRuns)
 
-      if self.debugMode: print "input of this \"map\": ",dumpInput[i:i+self.cpunum]
+      if self.debugMode:
+        print("input of this \"map\": ",dumpInput[i:i+self.cpunum])
 
       # create job_server
       job_server = multiprocessing.Pool(processes = self.cpunum)
@@ -136,14 +165,16 @@ class lpp:
 
     endtime = time.time()
     if self.output:
-      print "wrote", listlen,"granular snapshots in VTK format"
+      print("wrote", listlen,"granular snapshots in VTK format")
-      print "time needed:",endtime-starttime,"sec"
+      print("time needed:",endtime-starttime,"sec")
 
 def lppWorker(input):
   flist = input["filelist"]
   debugMode = input["debugMode"]
   outfileName = input["output"]
   overwrite = input["overwrite"]
+  Nth = input["Nth"]
+  timesteps = input["timesteps"]
 
   flistlen = len(flist)
   # generate name of manyGran
@@ -184,8 +215,25 @@ def lppWorker(input):
   # call dump, vtk, manyGran on shortFlist
   try:
     d = dump({"filelist":shortFlist, "debugMode":debugMode})
+
+    if timesteps != "all":
+      tsteps = timesteps.split(",")
+      filterstring = ""
+      j = 1
+      for i in tsteps:
+        if j == 1:
+          filterstring = filterstring + "$t == " + str(i)
+        else:
+          filterstring = filterstring + " or $t == " + str(i)
+        j = j + 1
+      d.tselect.test(filterstring)
+    elif Nth != 1:
+      d.tselect.skip(Nth)
+    d.delete()
+
     v = vtk.vtk(d)
-    if debugMode: print "\nfileNums: ",d.fileNums,"\n"
+    if debugMode:
+      print("\nfileNums: ",d.fileNums,"\n")
     v.manyGran(granName,fileNos=d.fileNums,output=debugMode)
   except KeyboardInterrupt:
     raise
@@ -193,21 +241,24 @@ def lppWorker(input):
   return 0
 
 def printHelp():
-  print "usage: pizza [options] dump.example\n where dump.example is a filename",\
+  print("usage: pizza [options] dump.example\n where dump.example is a filename",\
-    "or regular expression passing all relevant dump files to pizza."
+    "or regular expression passing all relevant dump files to pizza.")
-  print "Important command line options:"
+  print("Important command line options:")
-  print "-o fname    : define output file name (default is liggghts + timestep number)"
+  print("-o fname    : define output file name (default is liggghts + timestep number)")
-  print "--chunksize : sets the chunksize, default: 8"
+  print("--chunksize : sets the chunksize, default: 8")
-  print "--cpunum    : sets the number of processes to start, default (and maximum)",\
+  print("--cpunum    : sets the number of processes to start, default (and maximum)",\
-    "is the amout of cpu cores avaliable at your system"
+    "is the amout of cpu cores avaliable at your system")
-  print "--help      : writes this help message and exits"
+  print("--help      : writes this help message and exits")
-  print "--no-overwrite: disables overwriting of already post-processed files."
+  print("--no-overwrite: disables overwriting of already post-processed files.")
-  print "For details, read README_GRANULAR.txt"
+  print("--timesteps: time steps to be converted, input as comma seperated list.")
+  print("--Nth: every Nth time step will be converted, cannot be combined with timesteps.")
+  print("For details, read README_GRANULAR.txt")
 
 if __name__ == "__main__":
   if len(sys.argv) > 1:
     # parse options
-    optlist, args = getopt.gnu_getopt(sys.argv[1:],'o:',['chunksize=','cpunum=','debug','help','quiet','no-overwrite'])
+    optlist, args = getopt.gnu_getopt(sys.argv[1:],'o:',[
+                                          'chunksize=','cpunum=','Nth=','timesteps=','debug','help','quiet','no-overwrite'])
     optdict = dict(optlist)
     if "--help" in optdict:
       printHelp()
@@ -215,17 +266,17 @@ if __name__ == "__main__":
       try:
         lpp(args,**optdict)
       except KeyboardInterrupt:
-        print "aborted by user"
+        print("aborted by user")
-      except BaseException, e:
+      except BaseException as e:
-        print "aborting due to errors:", e
+        print("aborting due to errors:", e)
 
-    #===========================================================================
+    # ===========================================================================
     # except:
     #  if sys.exc_type == exceptions.SystemExit:
     #    pass
     #  else:
-    #    print sys.exc_info()
+    #    print(sys.exc_info())
-    #===========================================================================
+    # ===========================================================================
   else:
     printHelp()
 

src/matlab.py

@@ -8,15 +8,20 @@
 
 # matlab tool
 
+# Imports and external programs
+
+from __future__ import print_function, division, absolute_import
+import types, os
+
 oneline = "Create plots via MatLab numerical analysis program"
 
 docstr = """
-m = matlab()		       start up MatLab
+m = matlab()                   start up MatLab
-m.stop()		       shut down MatLab process
+m.stop()                       shut down MatLab process
 
 m.plot(a)                      plot vector A against linear index
-m.plot(a,b)	 	       plot B against A
+m.plot(a,b)                    plot B against A
-m.plot(a,b,c,d,...)	       plot B against A, D against C, etc
+m.plot(a,b,c,d,...)            plot B against A, D against C, etc
 m.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
   each plot argument can be a tuple, list, or Numeric/NumPy vector
@@ -29,9 +34,9 @@ m.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
 m("c = a + b")                 execute string in MatLab
 
-m.enter()	   	       enter MatLab shell
+m.enter()                      enter MatLab shell
 matlab> c = a + b              type commands directly to MatLab
-matlab> exit, quit	       exit MatLab shell
+matlab> exit, quit             exit MatLab shell
 
 m.export("data",range(100),a,...)       create file with columns of numbers
 
@@ -40,12 +45,12 @@ m.export("data",range(100),a,...)       create file with columns of numbers
     cols = importdata('data')
     plot(cols(:,1),cols(:,2))
 
-m.select(N)  	               figure N becomes the current plot
+m.select(N)                    figure N becomes the current plot
 
   subsequent commands apply to this plot
 
-m.hide(N)  	               delete window for figure N
+m.hide(N)                      delete window for figure N
-m.save("file")	               save current plot as file.eps
+m.save("file")                 save current plot as file.eps
 
 Set attributes for current plot:
 
@@ -91,10 +96,6 @@ m.curve(N,'b','-','v')         set color, line style, symbol of curve N
 #   allow for alternate export command to name the variables from Python
 #     in MatLab and vice versa
 
-# Imports and external programs
-
-import types, os
-
 try: from DEFAULTS import PIZZA_MATLAB
 except: PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm"
 
@@ -126,7 +127,7 @@ class matlab:
 
   def enter(self):
     while 1:
-      command = raw_input("matlab> ")
+      command = input("matlab> ")
       if command == "quit" or command == "exit": return
       self.__call__(command)
 
@@ -136,15 +137,15 @@ class matlab:
   def plot(self,*vectors):
     if len(vectors) == 1:
       file = self.file + ".%d.1" % self.current
-      linear = range(len(vectors[0]))
+      linear = list(range(len(vectors[0])))
       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)
+        file = self.file + ".%d.%d" % (self.current,i//2+1)
         self.export(file,vectors[i],vectors[i+1])
-      self.figures[self.current-1].ncurves = len(vectors)/2
+      self.figures[self.current-1].ncurves = len(vectors)//2
     self.draw()
 
   # --------------------------------------------------------------------
@@ -174,13 +175,13 @@ class matlab:
   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(vectors[j][i], end=' ', file=f)
-      print >>f
+      print(file=f)
     f.close()
 
   # --------------------------------------------------------------------

src/mdump.py

@@ -8,17 +8,25 @@
 
 # mdump tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, types
+import functools
+from os import popen
+from math import *             # any function could be used by set()
+
 oneline = "Read, write, manipulate mesh dump files"
 
 docstr = """
 m = mdump("mesh.one")             read in one or more mesh dump files
-m = mdump("mesh.1 mesh.2.gz")	  can be gzipped
+m = mdump("mesh.1 mesh.2.gz")     can be gzipped
-m = mdump("mesh.*")		  wildcard expands to multiple files
+m = mdump("mesh.*")               wildcard expands to multiple files
-m = mdump("mesh.*",0)		  two args = store filenames, but don't read
+m = mdump("mesh.*",0)             two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
 
-time = m.next()             	  read next snapshot from dump files
+time = m.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -28,20 +36,20 @@ time = m.next()             	  read next snapshot from dump files
 
 m.map(2,"temperature")            assign names to element value columns (1-N)
 
-m.tselect.all()			  select all timesteps
+m.tselect.all()                   select all timesteps
-m.tselect.one(N)		  select only timestep N
+m.tselect.one(N)                  select only timestep N
-m.tselect.none()		  deselect all timesteps
+m.tselect.none()                  deselect all timesteps
-m.tselect.skip(M)		  select every Mth step
+m.tselect.skip(M)                 select every Mth step
 m.tselect.test("$t >= 100 and $t < 10000")      select matching timesteps
-m.delete()	      	      	  delete non-selected timesteps
+m.delete()                        delete non-selected timesteps
 
   selecting a timestep also selects all elements in the timestep
   skip() and test() only select from currently selected timesteps
   test() uses a Python Boolean expression with $t for timestep value
     Python comparison syntax: == != < > <= >= and or
 
-m.eselect.all()	      	                      select all elems in all steps
+m.eselect.all()                               select all elems in all steps
-m.eselect.all(N)      	                      select all elems in one step
+m.eselect.all(N)                              select all elems in one step
 m.eselect.test("$id > 100 and $type == 2")    select match elems in all steps
 m.eselect.test("$id > 100 and $type == 2",N)  select matching elems in one step
 
@@ -52,7 +60,7 @@ m.eselect.test("$id > 100 and $type == 2",N)  select matching elems in one step
     Python comparison syntax: == != < > <= >= and or
     $name must end with a space
 
-t = m.time()  	     	       	   return vector of selected timestep values
+t = m.time()                        return vector of selected timestep values
 fx,fy,... = m.vecs(1000,"fx","fy",...)  return vector(s) for timestep N
 
   vecs() returns vectors with one value for each selected elem in the timestep
@@ -124,12 +132,6 @@ m.etype = "color"                          set column returned as "type" by viz
 #     nevalues = # of node values
 #     evalues[i][j] = 2d array of floats, i = 0 to Nel-1, j = 0 to Ncol
 
-# Imports and external programs
-
-import sys, commands, re, glob, types
-from os import popen
-from math import *             # any function could be used by set()
-
 try:
     import numpy as np
     oldnumeric = False
@@ -160,7 +162,7 @@ class mdump:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no dump file specified"
+      raise Exception("no dump file specified")
 
     if len(list) == 1:
       self.increment = 0
@@ -185,16 +187,16 @@ class mdump:
       snap = self.read_snapshot(f)
       while snap:
         self.snaps.append(snap)
-        print snap.time,
+        print(snap.time, end=' ')
         sys.stdout.flush()
         snap = self.read_snapshot(f)
 
       f.close()
-    print
+    print()
 
     # sort entries by timestep, cull and combine duplicates
 
-    self.snaps.sort(self.compare_time)
+    self.snaps.sort(key = functools.cmp_to_key(self.compare_time))
     self.cull()
 
     # sort all node, element, nvalue, evalue arrays by ID
@@ -204,25 +206,25 @@ class mdump:
         array = snap.nodes
         ids = array[:,0]
         ordering = np.argsort(ids)
-        for i in xrange(len(array[0])):
+        for i in range(len(array[0])):
           array[:,i] = np.take(array[:,i],ordering)
       if snap.eflag:
         array = snap.elements
         ids = array[:,0]
         ordering = np.argsort(ids)
-        for i in xrange(len(array[0])):
+        for i in range(len(array[0])):
           array[:,i] = np.take(array[:,i],ordering)
       if snap.nvalueflag:
         array = snap.nvalues
         ids = array[:,0]
         ordering = np.argsort(ids)
-        for i in xrange(len(array[0])):
+        for i in range(len(array[0])):
           array[:,i] = np.take(array[:,i],ordering)
       if snap.evalueflag:
         array = snap.evalues
         ids = array[:,0]
         ordering = np.argsort(ids)
-        for i in xrange(len(array[0])):
+        for i in range(len(array[0])):
           array[:,i] = np.take(array[:,i],ordering)
 
     # reference definitions of nodes and elements in previous timesteps
@@ -230,7 +232,7 @@ class mdump:
     self.reference()
 
     self.nsnaps = len(self.snaps)
-    print "read %d snapshots" % self.nsnaps
+    print("read %d snapshots" % self.nsnaps)
 
     # select all timesteps and elements
 
@@ -241,7 +243,7 @@ class mdump:
 
   def next(self):
 
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     # read next snapshot in current file using eof as pointer
     # if fail, try next file
@@ -253,15 +255,15 @@ class mdump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
+        self.eof = 0
-	continue
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     # select the new snapshot with all its elements
@@ -271,7 +273,7 @@ class mdump:
     snap.tselect = 1
     snap.nselect = snap.nelements
     if snap.eflag:
-      for i in xrange(snap.nelements): snap.eselect[i] = 1
+      for i in range(snap.nelements): snap.eselect[i] = 1
     self.nsnaps += 1
     self.nselect += 1
 
@@ -295,7 +297,7 @@ class mdump:
       elif "NUMBER OF CUBES" in str: snap.eflag = 4
       elif "NUMBER OF NODE VALUES" in str: snap.nvalueflag = 1
       elif "NUMBER OF ELEMENT VALUES" in str: snap.evalueflag = 1
-      else: raise StandardError,"unrecognized snapshot in dump file"
+      else: raise Exception("unrecognized snapshot in dump file")
       n = int(f.readline())
 
       if snap.eflag: snap.eselect = np.zeros(n)
@@ -313,14 +315,14 @@ class mdump:
       if n:
         words = f.readline().split()
         ncol = len(words)
-        for i in xrange(1,n):
+        for i in range(1,n):
           words += f.readline().split()
-        floats = map(float,words)
+        floats = list(map(float,words))
         if oldnumeric: values = np.zeros((n,ncol),np.Float)
         else: values = np.zeros((n,ncol),np.float)
         start = 0
         stop = ncol
-        for i in xrange(n):
+        for i in range(n):
           values[i] = floats[start:stop]
           start = stop
           stop += ncol
@@ -343,7 +345,7 @@ class mdump:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "mdump map() requires pairs of mappings"
+      raise Exception("mdump map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -360,15 +362,15 @@ class mdump:
         self.nsnaps -= 1
         ndel += 1
       else: i += 1
-    print "%d snapshots deleted" % ndel
+    print("%d snapshots deleted" % ndel)
-    print "%d snapshots remaining" % self.nsnaps
+    print("%d snapshots remaining" % self.nsnaps)
 
   # --------------------------------------------------------------------
   # sort elements by ID in all selected timesteps or one timestep
 
   def sort(self,*list):
     if len(list) == 0:
-      print "Sorting selected snapshots ..."
+      print("Sorting selected snapshots ...")
       id = self.names["id"]
       for snap in self.snaps:
         if snap.tselect: self.sort_one(snap,id)
@@ -385,7 +387,7 @@ class mdump:
     atoms = snap.atoms
     ids = atoms[:,id]
     ordering = np.argsort(ids)
-    for i in xrange(len(atoms[0])):
+    for i in range(len(atoms[0])):
       atoms[:,i] = np.take(atoms[:,i],ordering)
 
   # --------------------------------------------------------------------
@@ -406,10 +408,10 @@ class mdump:
   def vecs(self,n,*list):
     snap = self.snaps[self.findtime(n)]
     if not snap.evalues:
-      raise StandardError, "snapshot has no element values"
+      raise Exception("snapshot has no element values")
 
     if len(list) == 0:
-      raise StandardError, "no columns specified"
+      raise Exception("no columns specified")
     columns = []
     values = []
     for name in list:
@@ -418,9 +420,9 @@ class mdump:
     ncol = len(columns)
 
     m = 0
-    for i in xrange(len(snap.evalues)):
+    for i in range(len(snap.evalues)):
       if not snap.eselect[i]: continue
-      for j in xrange(ncol):
+      for j in range(ncol):
         values[j][m] = snap.evalues[i][columns[j]]
       m += 1
 
@@ -482,9 +484,9 @@ class mdump:
   # if not, point it at most recent shapshot that does
 
   def reference(self):
-    for i in xrange(len(self.snaps)):
+    for i in range(len(self.snaps)):
       if not self.snaps[i].nflag:
-        for j in xrange(i,-1,-1):
+        for j in range(i,-1,-1):
           if self.snaps[j].nflag:
             self.snaps[i].nflag = self.snaps[j].nflag
             self.snaps[i].nnodes = self.snaps[j].nnodes
@@ -497,9 +499,9 @@ class mdump:
             self.snaps[i].zhi = self.snaps[j].zhi
             break
       if not self.snaps[i].nflag:
-        raise StandardError,"no nodal coords found in previous snapshots"
+        raise Exception("no nodal coords found in previous snapshots")
       if not self.snaps[i].eflag:
-        for j in xrange(i,-1,-1):
+        for j in range(i,-1,-1):
           if self.snaps[j].eflag:
             self.snaps[i].eflag = self.snaps[j].eflag
             self.snaps[i].nelements = self.snaps[j].nelements
@@ -507,7 +509,7 @@ class mdump:
             self.snaps[i].eselect = self.snaps[j].eselect
             break
       if not self.snaps[i].eflag:
-        raise StandardError,"no elem connections found in previous snapshots"
+        raise Exception("no elem connections found in previous snapshots")
 
   # --------------------------------------------------------------------
   # iterate over selected snapshots
@@ -515,7 +517,7 @@ class mdump:
   def iterator(self,flag):
     start = 0
     if flag: start = self.iterate + 1
-    for i in xrange(start,self.nsnaps):
+    for i in range(start,self.nsnaps):
       if self.snaps[i].tselect:
         self.iterate = i
         return i,self.snaps[i].time,1
@@ -550,7 +552,7 @@ class mdump:
 
     tris = []
     nodes = snap.nodes
-    for i in xrange(snap.nelements):
+    for i in range(snap.nelements):
       if not snap.eselect[i]: continue
       element = snap.elements[i]
       if snap.evalueflag: evalue = snap.evalues[i]
@@ -699,9 +701,9 @@ class mdump:
   # --------------------------------------------------------------------
 
   def findtime(self,n):
-    for i in xrange(self.nsnaps):
+    for i in range(self.nsnaps):
       if self.snaps[i].time == n: return i
-    raise StandardError, "no step %d exists" % n
+    raise Exception("no step %d exists" % n)
 
   # --------------------------------------------------------------------
   # return maximum box size across all selected snapshots
@@ -751,7 +753,7 @@ class tselect:
       snap.tselect = 1
     data.nselect = len(data.snaps)
     data.eselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -763,7 +765,7 @@ class tselect:
     data.snaps[i].tselect = 1
     data.nselect = 1
     data.eselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -772,7 +774,7 @@ class tselect:
     for snap in data.snaps:
       snap.tselect = 0
     data.nselect = 0
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -788,7 +790,7 @@ class tselect:
       snap.tselect = 0
       data.nselect -= 1
     data.eselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
   # --------------------------------------------------------------------
 
@@ -797,14 +799,16 @@ class tselect:
     snaps = data.snaps
     cmd = "flag = " + teststr.replace("$t","snaps[i].time")
     ccmd = compile(cmd,'','single')
-    for i in xrange(data.nsnaps):
+    for i in range(data.nsnaps):
       if not snaps[i].tselect: continue
-      exec ccmd
+      ldict = {'data':data,'snaps':snaps,'i':i}
+      exec(ccmd,globals(),ldict)
+      flag = ldict['flag']
       if not flag:
         snaps[i].tselect = 0
         data.nselect -= 1
     data.eselect.all()
-    print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
+    print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
 
 # --------------------------------------------------------------------
 # element selection class
@@ -821,12 +825,12 @@ class eselect:
     if len(args) == 0:                           # all selected timesteps
       for snap in data.snaps:
         if not snap.tselect: continue
-        for i in xrange(snap.nelements): snap.eselect[i] = 1
+        for i in range(snap.nelements): snap.eselect[i] = 1
         snap.nselect = snap.nelements
     else:                                        # one timestep
       n = data.findtime(args[0])
       snap = data.snaps[n]
-      for i in xrange(snap.nelements): snap.eselect[i] = 1
+      for i in range(snap.nelements): snap.eselect[i] = 1
       snap.nselect = snap.nelements
 
   # --------------------------------------------------------------------
@@ -849,29 +853,29 @@ class eselect:
     if len(args) == 0:                           # all selected timesteps
       for snap in data.snaps:
         if not snap.tselect: continue
-        for i in xrange(snap.nelements):
+        for i in range(snap.nelements):
           if not snap.eselect[i]: continue
-          exec ccmd
+          exec(ccmd)
           if not flag:
             snap.eselect[i] = 0
             snap.nselect -= 1
-      for i in xrange(data.nsnaps):
+      for i in range(data.nsnaps):
         if data.snaps[i].tselect:
-          print "%d atoms of %d selected in first step %d" % \
+          print("%d atoms of %d selected in first step %d" % \
-                (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time)
+                (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time))
           break
-      for i in xrange(data.nsnaps-1,-1,-1):
+      for i in range(data.nsnaps-1,-1,-1):
         if data.snaps[i].tselect:
-          print "%d atoms of %d selected in last step %d" % \
+          print("%d atoms of %d selected in last step %d" % \
-                (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time)
+                (data.snaps[i].nselect,data.snaps[i].nelements,data.snaps[i].time))
           break
 
     else:                                        # one timestep
       n = data.findtime(args[0])
       snap = data.snaps[n]
-      for i in xrange(snap.nelements):
+      for i in range(snap.nelements):
         if not snap.eselect[i]: continue
-        exec ccmd
+        exec(ccmd)
         if not flag:
           snap.eselect[i] = 0
           snap.nselect -= 1

src/pair.py

@@ -8,6 +8,11 @@
 
 # pair tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+from math import sqrt
+
 oneline = "Compute LAMMPS pairwise energies"
 
 docstr = """
@@ -15,8 +20,8 @@ p = pair("lj/charmm/coul/charmm")   create pair object for specific pair style
 
   available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm
 
-p.coeff(d)			    extract pairwise coeffs from data object
+p.coeff(d)                          extract pairwise coeffs from data object
-p.init(cut1,cut2,...)		    setup based on coeffs and cutoffs
+p.init(cut1,cut2,...)               setup based on coeffs and cutoffs
 
   init args are specific to pair style:
     lj/cut = cutlj
@@ -41,10 +46,6 @@ e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...)   compute LJ/Coul energy
 
 # Variables
 
-# Imports and external programs
-
-from math import sqrt
-
 # Class definition
 
 class pair:
@@ -68,7 +69,7 @@ class pair:
       self.init_func = self.init_lj_charmm_coul_charmm
       self.single_func = self.single_lj_charmm_coul_charmm
     else:
-      raise StandardError, "this pair style not yet supported"
+      raise Exception("this pair style not yet supported")
 
   # --------------------------------------------------------------------
   # generic coeff method
@@ -99,10 +100,10 @@ class pair:
 
     self.lj3 = []
     self.lj4 = []
-    for i in xrange(ntypes):
+    for i in range(ntypes):
       self.lj3.append(ntypes * [0])
       self.lj4.append(ntypes * [0])
-      for j in xrange(ntypes):
+      for j in range(ntypes):
         epsilon_ij = sqrt(epsilon[i]*epsilon[j])
         sigma_ij = sqrt(sigma[i]*sigma[j])
         self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
@@ -143,10 +144,10 @@ class pair:
 
     self.lj3 = []
     self.lj4 = []
-    for i in xrange(ntypes):
+    for i in range(ntypes):
       self.lj3.append(ntypes * [0])
       self.lj4.append(ntypes * [0])
-      for j in xrange(ntypes):
+      for j in range(ntypes):
         epsilon_ij = sqrt(epsilon[i]*epsilon[j])
         sigma_ij = sqrt(sigma[i]*sigma[j])
         self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
@@ -156,7 +157,7 @@ class pair:
   # args = cutlj, cut_coul (cut_coul optional)
 
   def init_lj_cut_coul_cut(self,list):
-    self.qqr2e = 332.0636  			# convert energy to kcal/mol
+    self.qqr2e = 332.0636                       # convert energy to kcal/mol
     cut_lj = list[0]
     self.cut_ljsq = cut_lj*cut_lj
 
@@ -197,10 +198,10 @@ class pair:
 
     self.lj3 = []
     self.lj4 = []
-    for i in xrange(ntypes):
+    for i in range(ntypes):
       self.lj3.append(ntypes * [0])
       self.lj4.append(ntypes * [0])
-      for j in xrange(ntypes):
+      for j in range(ntypes):
         epsilon_ij = sqrt(epsilon[i]*epsilon[j])
         sigma_ij = 0.5 * (sigma[i] + sigma[j])
         self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
@@ -210,7 +211,7 @@ class pair:
   # args = cutlj_inner,cutlj,cutcoul_inner,cut_coul (last 2 optional)
 
   def init_lj_charmm_coul_charmm(self,list):
-    self.qqr2e = 332.0636  			# convert energy to kcal/mol
+    self.qqr2e = 332.0636                       # convert energy to kcal/mol
     cut_lj_inner = list[0]
     cut_lj = list[1]
 

src/patch.py

@@ -8,15 +8,21 @@
 
 # patch tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+from math import sqrt,pi,cos,sin
+from data import data
+
 oneline = "Create patchy Lennard-Jones particles for LAMMPS input"
 
 docstr = """
 p = patch(vfrac)           setup box with a specified volume fraction
 p = patch(vfrac,1,1,2)     x,y,z = aspect ratio of box (def = 1,1,1)
 
-p.seed = 48379		   set random # seed (def = 12345)
+p.seed = 48379             set random # seed (def = 12345)
-p.randomized = 0	   1 = choose next particle randomly, 0 = as generated
+p.randomized = 0           1 = choose next particle randomly, 0 = as generated
-p.dim = 2		   set dimension of created box (def = 3)
+p.dim = 2                  set dimension of created box (def = 3)
 p.blen = 0.97              set length of tether bonds (def = 0.97)
 p.dmin = 1.02              set min r from i-1 to i+1 tether site (def = 1.02)
 p.lattice = [Nx,Ny,Nz]     generate Nx by Ny by Nz lattice of particles
@@ -61,11 +67,6 @@ p.write("data.patch")      write out system to LAMMPS data file
 #   seed = random seed
 #   molecules = list of atoms, grouped by molecule
 
-# Imports and external programs
-
-from math import sqrt,pi,cos,sin
-from data import data
-
 # Class definition
 
 class patch:
@@ -98,8 +99,14 @@ class patch:
     if style == "linebox" or style == "linetri": self.style = "line"
     if style == "tritet" or style == "tribox": self.style = "tri"
     cmd = "atoms,bonds,tris,segments,volume = self.%s(*types)" % style
-    for i in xrange(n):
+    for i in range(n):
-      exec cmd
+      ldict = {'i':i,'self':self,'types':types}
+      exec(cmd,globals(),ldict)
+      atoms = ldict['atoms']
+      bonds = ldict['bonds']
+      tris = ldict['tris']
+      segments = ldict['segments']
+      volume = ldict['volume']
       self.molecules.append([atoms,bonds,tris,segments])
       self.volume += volume
 
@@ -131,7 +138,7 @@ class patch:
       latflag = 1
       if self.lattice[0]*self.lattice[1]*self.lattice[2] != \
              len(self.molecules):
-        raise StandardError,"lattice inconsistent with # of molecules"
+        raise Exception("lattice inconsistent with # of molecules")
     else: latflag = 0
 
     idatom = idbond = idtri = idmol = 0
@@ -343,7 +350,7 @@ class patch:
     if self.lattice[0] or self.lattice[1]:
       latflag = 1
       if self.lattice[0]*self.lattice[1] != len(self.molecules):
-        raise StandardError,"lattice inconsistent with # of molecules"
+        raise Exception("lattice inconsistent with # of molecules")
     else: latflag = 0
 
     idatom = idbond = idmol = 0
@@ -885,7 +892,7 @@ class patch:
     sep = params[1]
     type = params[2]
     if n % 2 == 0:
-      raise StandardError, "N in patch::star2d is not odd"
+      raise Exception("N in patch::star2d is not odd")
     middle = n/2
 
     atoms = []
@@ -1131,7 +1138,7 @@ class patch:
   # --------------------------------------------------------------------
 
   def random(self):
-    k = self.seed/IQ
+    k = self.seed//IQ
     self.seed = IA*(self.seed-k*IQ) - IR*k
     if self.seed < 0:
       self.seed += IM

src/pdbfile.py

@@ -8,6 +8,15 @@
 
 # pdb tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, types, glob
+try:
+  import urllib.request, urllib.parse, urllib.error
+except ImportError:
+  import urllib
+
 oneline = "Read, write PDB files in combo with LAMMPS snapshots"
 
 docstr = """
@@ -62,10 +71,6 @@ index,time,flag = p.iterator(1)
 #   atomlines = dict of ATOM lines in original PDB file
 #     key = atom id, value = tuple of (beginning,end) of line
 
-# Imports and external programs
-
-import sys, types, glob, urllib
-
 # Class definition
 
 class pdbfile:
@@ -74,7 +79,7 @@ class pdbfile:
 
   def __init__(self,*args):
     if len(args) == 1:
-      if type(args[0]) is types.StringType:
+      if type(args[0]) is bytes:
         filestr = args[0]
         self.data = None
       else:
@@ -83,7 +88,7 @@ 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 +99,17 @@ 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
 
@@ -112,9 +117,9 @@ 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])
+        urllib.request.urlretrieve(fetchstr,self.files[0])
 
     if self.data and len(self.files): self.read_template(self.files[0])
 
@@ -142,20 +147,20 @@ 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 +195,7 @@ class pdbfile:
         self.convert(f,which)
         f.close()
 
-        print time,
+        print(time, end=' ')
         sys.stdout.flush()
         n += 1
 
@@ -210,12 +215,12 @@ 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
@@ -277,13 +282,13 @@ class pdbfile:
     if len(self.files):
       for atom in atoms:
         id = atom[0]
-        if self.atomlines.has_key(id):
+        if id in self.atomlines:
           (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, end=' ', file=f)
     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)

src/pizza.py

@@ -15,6 +15,12 @@
 
 # ToDo list:
 
+# modules needed by pizza.py
+
+from __future__ import print_function, absolute_import
+import sys, os, string, glob, re
+import time
+
 # Help strings:
 
 version = "LPP 1.0 based on pizza - 7 Oct 2011"
@@ -26,12 +32,12 @@ type ? for help, CTRL-D to quit
 
 help = """
 pizza.py switch arg(s) switch arg(s) ...
-  -s	 	              silent (else print start-up help)
+  -s                          silent (else print start-up help)
-  -t log dump raster	      load only these tools
+  -t log dump raster          load only these tools
-  -x raster rasmol	      load all tools except these
+  -x raster rasmol            load all tools except these
   -f mine.py arg1 arg2        run script file with args
-  -c "vec = range(100)"	      run Python command
+  -c "vec = range(100)"       run Python command
-  -q 	   		      quit (else interactive)
+  -q                          quit (else interactive)
 
 Everything typed at the ">" prompt is a Python command
 
@@ -50,18 +56,13 @@ Tools:
 """
 
 # -------------------------------------------------------------------------
-# modules needed by pizza.py
-
-import sys, commands, os, string, exceptions, glob, re
-from time import clock
-
 # readline not available in all Pythons
 
 try:
   import readline
   readline_flag = 1
-except ImportError, exception:
+except ImportError as exception:
-  print "readline option not available"
+  print("readline option not available")
   readline_flag = 0
 
 # create global Tk root if Tkinter is loaded
@@ -72,10 +73,12 @@ try:
   import Tkinter
   tkroot = Tkinter.Tk()
   tkroot.withdraw()
-except ImportError, exception:
+except ImportError as exception:
-  nodisplay = True
+  import tkinter
+  tkroot = tkinter.Tk()
+  tkroot.withdraw()
   pass
-except Exception, exception:
+except Exception as exception:
   nodisplay = True
   pass
 
@@ -107,22 +110,22 @@ def trap(type,value,tback):
      words = value.text.split()
 
      if len(words) == 1 and words[0] == "?":
-       print intro[1:] % version
+       print(intro[1:] % version)
-       print help[1:]," ",
+       print(help[1:]," ", end=' ')
-       for tool in tools: print tool,
+       for tool in tools: print(tool, end=' ')
-       print
+       print()
 
      elif len(words) == 1 and words[0] == "??":
        for tool in tools:
-         exec "oneline = oneline_%s" % tool
+         exec("oneline = oneline_%s" % tool)
-         print "%-11s%s" % (tool,oneline)
+         print("%-11s%s" % (tool,oneline))
-       print
+       print()
 
        scripts = []
        for dir in PIZZA_SCRIPTS[1:]:
-         list = glob.glob("%s/*.py" % dir)
+         flist = glob.glob("%s/*.py" % dir)
-         list.sort()
+         flist.sort()
-         scripts += list
+         scripts += flist
        for script in scripts:
          filename = os.path.basename(script)
          lines = open(script,'r').readlines()
@@ -133,7 +136,7 @@ def trap(type,value,tback):
              break
          if flag: doc = line[line.find("Purpose:")+8:]
          else: doc = " not available\n"
-         print "%-20s%s" % (filename,doc),
+         print("%-20s%s" % (filename,doc), end=' ')
 
      elif len(words) == 2 and words[0] == "?":
        if words[1][-3:] == ".py":
@@ -145,25 +148,25 @@ def trap(type,value,tback):
              lineflag = 0
              lines = open(filename,'r').readlines()
              for line in lines:
-               if line.find("# Purpose:") >= 0: print line[2:],
+               if line.find("# Purpose:") >= 0: print(line[2:], end=' ')
                if line.find("# Syntax:") >= 0:
                  lineflag = 1
                  break
-             if not lineflag: print "%s has no Syntax line" % words[1]
+             if not lineflag: print("%s has no Syntax line" % words[1])
-             else: print line[2:],
+             else: print(line[2:], end=' ')
              break
          if not fileflag:
-           print "%s is not a recognized script" % words[1]
+           print("%s is not a recognized script" % words[1])
 
        else:
          if words[1] in tools:
-           exec "txt = docstr_%s" % words[1]
+           exec("txt = docstr_%s" % words[1])
            txt = re.sub("\n\s*\n","\n",txt)
            txt = re.sub("\n .*","",txt)
-           exec "print oneline_%s" % words[1]
+           exec("print oneline_%s" % words[1])
-           print txt
+           print(txt)
          else:
-           print "%s is not a recognized tool" % words[1]
+           print("%s is not a recognized tool" % words[1])
 
      elif len(words) == 2 and words[0] == "??":
        if words[1][-3:] == ".py":
@@ -175,18 +178,18 @@ def trap(type,value,tback):
              lines = open(filename,'r').readlines()
              for line in lines:
                if len(line.strip()) == 0: continue
-               if line[0] == '#': print line,
+               if line[0] == '#': print(line, end=' ')
                else: break
              break
          if not fileflag:
-           print "%s is not a recognized script" % words[1]
+           print("%s is not a recognized script" % words[1])
 
        else:
          if words[1] in tools:
-           exec "print oneline_%s" % words[1]
+           exec("print oneline_%s" % words[1])
-           exec "print docstr_%s" % words[1]
+           exec("print docstr_%s" % words[1])
          else:
-           print "%s is not a recognized class" % words[1]
+           print("%s is not a recognized class" % words[1])
 
      return
 
@@ -208,13 +211,13 @@ def trap(type,value,tback):
        return
      elif words[0][1:] == "log":
        if readline_flag == 0:
-         print "cannot use @log without readline module"
+         print("cannot use @log without readline module")
          return
        f = open(words[1],"w")
-       print >>f,"# pizza.py log file\n"
+       print("# pizza.py log file\n", file=f)
        nlines = readline.get_current_history_length()
-       for i in xrange(1,nlines):
+       for i in range(1,nlines):
-         print >>f,readline.get_history_item(i)
+         print(readline.get_history_item(i), file=f)
        f.close()
        return
      elif words[0][1:] == "run":
@@ -225,17 +228,17 @@ def trap(type,value,tback):
          fullfile = dir + '/' + file
          if os.path.exists(fullfile):
            flag = 1
-           print "Executing file:",fullfile
+           print("Executing file:",fullfile)
-           execfile(fullfile,namespace)
+           exec(compile(open(fullfile).read(), fullfile, 'exec'),namespace)
            break
-       if not flag: print "Could not find file",file
+       if not flag: print("Could not find file",file)
        return
      elif words[0][1:] == "time":
        cmd = string.join(words[1:])
        t1 = clock()
-       exec cmd in namespace
+       exec(cmd, namespace)
        t2 = clock()
-       print "CPU time = ",t2-t1
+       print("CPU time = ",t2-t1)
        return
 
    # unrecognized command, let system handle error
@@ -255,7 +258,7 @@ quitflag = 0
 iarg = 1
 while (iarg < len(sys.argv)):
   if (sys.argv[iarg][0] != '-'):
-    print "ERROR: arg is not a switch: %s" % (sys.argv[iarg])
+    print("ERROR: arg is not a switch: %s" % (sys.argv[iarg]))
     sys.exit()
   if (sys.argv[iarg] == "-s"):
     silent = 1
@@ -274,37 +277,37 @@ while (iarg < len(sys.argv)):
     iarg = jarg
   elif (sys.argv[iarg] == "-f"):
     jarg = iarg + 1
-    list = []
+    flist = []
     while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'):
-      list.append(sys.argv[jarg])
+      flist.append(sys.argv[jarg])
       jarg += 1
-    task = ("script",list)
+    task = ("script",flist)
     tasks.append(task)
     iarg = jarg
   elif (sys.argv[iarg] == "-c"):
     jarg = iarg + 1
-    list = []
+    clist = []
     while (jarg < len(sys.argv) and sys.argv[jarg][0] != '-'):
-      list.append(sys.argv[jarg])
+      clist.append(sys.argv[jarg])
       jarg += 1
-    task = ("command",list)
+    task = ("command",clist)
     tasks.append(task)
     iarg = jarg
   elif (sys.argv[iarg] == "-q"):
     quitflag = 1
     iarg += 1
   else:
-    print "ERROR: unknown switch: %s" % (sys.argv[iarg])
+    print("ERROR: unknown switch: %s" % (sys.argv[iarg]))
     sys.exit()
 
 # print intro message
 
-if not silent: print intro[1:] % version,
+if not silent: print(intro[1:] % version, end=' ')
 
 # error test on m,x command-line switches
 
 if len(yes_tools) > 0 and len(no_tools) > 0:
-  print "ERROR: cannot use -t and -x switches together"
+  print("ERROR: cannot use -t and -x switches together")
   sys.exit()
 
 # -------------------------------------------------------------------------
@@ -313,12 +316,12 @@ if len(yes_tools) > 0 and len(no_tools) > 0:
 # else scan for *.py files in all dirs in PIZZA_TOOLS list
 #   and then Pizza.py src dir (sys.path[0])
 
-if not silent: print "Loading tools ..."
+if not silent: print("Loading tools ...")
-if not silent and nodisplay: print "Display not available ... no GUIs"
+if not silent and nodisplay: print("Display not available ... no GUIs")
 
 try: from DEFAULTS import PIZZA_TOOLS
 except: PIZZA_TOOLS = []
-PIZZA_TOOLS = map(os.path.expanduser,PIZZA_TOOLS)
+PIZZA_TOOLS = list(map(os.path.expanduser,PIZZA_TOOLS))
 PIZZA_TOOLS.append(sys.path[0])
 
 if len(yes_tools) > 0: tools = yes_tools
@@ -359,12 +362,12 @@ for tool in tools:
     failed.append(tool)
     continue
   try:
-    exec "from %s import %s" % (tool,tool)
+    exec("from %s import %s" % (tool,tool))
-    exec "from %s import oneline as oneline_%s" % (tool,tool)
+    exec("from %s import oneline as oneline_%s" % (tool,tool))
-    exec "from %s import docstr as docstr_%s" % (tool,tool)
+    exec("from %s import docstr as docstr_%s" % (tool,tool))
-  except Exception, exception:
+  except Exception as exception:
-    print "%s tool did not load:" % tool
+    print("%s tool did not load:" % tool)
-    print " ",exception
+    print(" ",exception)
     failed.append(tool)
 
 for dir in PIZZA_TOOLS: sys.path = sys.path[1:]
@@ -384,7 +387,7 @@ sys.path.insert(0,'')
 
 try: from DEFAULTS import PIZZA_SCRIPTS
 except: PIZZA_SCRIPTS = []
-PIZZA_SCRIPTS = map(os.path.expanduser,PIZZA_SCRIPTS)
+PIZZA_SCRIPTS = list(map(os.path.expanduser,PIZZA_SCRIPTS))
 PIZZA_SCRIPTS.insert(0,'.')
 PIZZA_SCRIPTS.append(sys.path[1][:-3] + "scripts")   # path for pizza.py
 
@@ -403,27 +406,27 @@ for task in tasks:
       for dir in PIZZA_SCRIPTS:
         fullfile = dir + '/' + file
         if os.path.exists(fullfile):
-          print "Executing file:",fullfile
+          print("Executing file:",fullfile)
-          execfile(fullfile)
+          exec(compile(open(fullfile).read(), fullfile, 'exec'))
           flag = 1
           break
-      if not flag: print "Could not find file",file
+      if not flag: print("Could not find file",file)
-    except StandardError, exception:
+    except Exception as exception:
       (type,value,tback) = sys.exc_info()
-      print type,value,tback
+      print(type,value,tback)
       type = str(type)
       type = type[type.find(".")+1:]
-      print "%s with value: %s" % (type,value)
+      print("%s with value: %s" % (type,value))
       tback = tback.tb_next
       while tback:
-        print "error on line %d of file %s" % \
+        print("error on line %d of file %s" % \
-              (tback.tb_lineno,tback.tb_frame.f_code.co_filename)
+              (tback.tb_lineno,tback.tb_frame.f_code.co_filename))
         tback = tback.tb_next
   elif task[0] == "command":
     argv = task[1]
     cmd = ""
     for arg in argv: cmd += arg + " "
-    exec cmd
+    exec(cmd)
 
 # -------------------------------------------------------------------------
 # store global namespace

src/plotview.py

@@ -8,6 +8,15 @@
 
 # plotview tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, time
+try:
+  from Tkinter import *
+except ImportError:
+  from tkinter import *
+
 oneline = "Plot multiple vectors from a data set"
 
 docstr = """
@@ -46,11 +55,6 @@ p.save()                save currently selected plot to file.eps
 #   checkvars = list of status of check buttons
 #   checkold = list of status of check buttons before click
 
-# Imports and external programs
-
-import sys, re, glob, time
-from Tkinter import *
-
 # Class definition
 
 class plotview:
@@ -148,7 +152,7 @@ class plotview:
 
   def save(self):
     n = self.radiovar.get()
-    if n == 0: raise StandardError,"no plot selected"
+    if n == 0: raise Exception("no plot selected")
     name = self.entry.get()
     self.plot.save(name)
 

src/rasmol.py

@@ -8,6 +8,16 @@
 
 # rasmol tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, os, re, types
+try:
+  import commands
+except ImportError:
+  import subprocess as commands
+from pdbfile import pdbfile
+
 oneline = "3d visualization via RasMol program"
 
 docstr = """
@@ -38,11 +48,6 @@ r.run(N,"new.rasmol","old.rasmol")    type quit to save RasMol script file
 
 # Variables
 
-# Imports and external programs
-
-import sys, os, commands, re, types
-from pdbfile import pdbfile
-
 try: from DEFAULTS import PIZZA_RASMOL
 except: PIZZA_RASMOL = "rasmol"
 try: from DEFAULTS import PIZZA_DISPLAY
@@ -67,7 +72,7 @@ class rasmol:
 
   def enter(self):
     while 1:
-      command = raw_input("rasmol> ")
+      command = input("rasmol> ")
       if command == "quit" or command == "exit": return
       self.__call__(command)
 
@@ -85,19 +90,19 @@ class rasmol:
 
   # --------------------------------------------------------------------
 
-  def show(self,*list):
+  def show(self,*arglist):
 
     # create tmp.pdb with atom data
 
-    n = list[0]
+    n = arglist[0]
     self.pdb.single(n,"tmp.pdb")
 
     # if RasMol input script specified, read it
     # replace load pdb "file" with load pdb "%s"
     # if no RasMol input script specified, use rasmol_template
 
-    if len(list) == 2:
+    if len(arglist) == 2:
-      rasmol_text = open(list[1],"r").read()
+      rasmol_text = open(arglist[1],"r").read()
       rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text)
     else:
       rasmol_text = rasmol_template
@@ -106,7 +111,7 @@ class rasmol:
 
     f = open("tmp.rasmol","w")
     text = rasmol_text % "tmp.pdb"
-    print >>f,text
+    print(text, file=f)
     f.close()
 
     # run RasMol to create image in tmp.gif
@@ -123,14 +128,14 @@ class rasmol:
 
   # --------------------------------------------------------------------
 
-  def all(self,*list):
+  def all(self,*arglist):
 
     # if RasMol script specified, read it
     # replace load pdb "file" with load pdb "%s"
     # if no RasMol script specified, just use rasmol_template
 
-    if len(list) == 1:
+    if len(arglist) == 1:
-      rasmol_text = open(list[0],"r").read()
+      rasmol_text = open(arglist[0],"r").read()
       rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text)
     else:
       rasmol_text = rasmol_template
@@ -160,10 +165,10 @@ class rasmol:
       text = rasmol_text % file_pdb
       file_rasmol = "tmp%s.rasmol" % ncount
       f = open(file_rasmol,"w")
-      print >>f,text
+      print(text, file=f)
       f.close()
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
@@ -172,7 +177,7 @@ class rasmol:
     self.start()
 
     loop = n
-    for n in xrange(loop):
+    for n in range(loop):
       if n < 10:
         ncount = "000" + str(n)
       elif n < 100:
@@ -196,19 +201,19 @@ class rasmol:
 
   # --------------------------------------------------------------------
 
-  def run(self,*list):
+  def run(self,*arglist):
 
     # create tmp.pdb with atom data
 
-    n = list[0]
+    n = arglist[0]
     self.pdb.single(n,"tmp.pdb")
 
     # if RasMol script specified, read it
     # replace load pdb "file" with load pdb "%s"
     # if no RasMol script specified, just use rasmol_template
 
-    if len(list) == 3:
+    if len(arglist) == 3:
-      rasmol_text = open(list[2],"r").read()
+      rasmol_text = open(arglist[2],"r").read()
       rasmol_text = re.sub('load pdb ".*"','load pdb "%s"',rasmol_text)
     else:
       rasmol_text = rasmol_template
@@ -217,7 +222,7 @@ class rasmol:
 
     f = open("tmp.rasmol","w")
     text = rasmol_template % "tmp.pdb"
-    print >>f,text
+    print(text, file=f)
     f.close()
 
     # run RasMol to create image in tmp.gif
@@ -226,7 +231,7 @@ class rasmol:
     self.__call__("source tmp.rasmol")
     self.enter()
 
-    if len(list) > 1: newfile = list[1]
+    if len(arglist) > 1: newfile = arglist[1]
     else: newfile = "tmp.rasmol"
     self.__call__("write script %s" % newfile)
     self.stop()

src/raster.py

@@ -8,6 +8,17 @@
 
 # raster tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, os, re
+try:
+  import commands
+except ImportError:
+  import subprocess as commands
+from vizinfo import vizinfo
+from math import fabs,atan,cos,sin
+
 oneline = "3d visualization via Raster3d program"
 
 docstr = """
@@ -16,8 +27,8 @@ r = raster(d)               create Raster3d wrapper for data in d
   d = atom snapshot object (dump, data)
 
 r.bg("black")               set background color (def = "black")
-r.size(N)		    set image size to NxN
+r.size(N)                   set image size to NxN
-r.size(N,M)		    set image size to NxM
+r.size(N,M)                 set image size to NxM
 r.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
 r.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
 r.zoom(0.5)                 scale image by factor (def = 1)
@@ -49,9 +60,9 @@ r.nolabel()                                      delete all labels
   x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font
   size = fontsize (e.g. 10), "red" = color of text
 
-r.acol(2,"green")		   set atom colors by atom type (1-N)
+r.acol(2,"green")                  set atom colors by atom type (1-N)
-r.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+r.acol([2,4],["red","blue"])       1st arg = one type or list of types
-r.acol(0,"blue")	           2nd arg = one color or list of colors
+r.acol(0,"blue")                   2nd arg = one color or list of colors
 r.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
 r.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
@@ -61,19 +72,19 @@ r.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
 r.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol()
 
-r.bcol()			   set bond color, same args as acol()
+r.bcol()                           set bond color, same args as acol()
-r.brad()			   set bond thickness, same args as arad()
+r.brad()                           set bond thickness, same args as arad()
 
-r.tcol()			   set triangle color, same args as acol()
+r.tcol()                           set triangle color, same args as acol()
-r.tfill()			   set triangle fill, 0 fill, 1 line, 2 both
+r.tfill()                          set triangle fill, 0 fill, 1 line, 2 both
 
 r.lcol()                           set line color, same args as acol()
 r.lrad()                           set line thickness, same args as arad()
 
 r.adef()                           set atom/bond/tri/line properties to default
-r.bdef()			   default = "loop" for colors, 0.45 for radii
+r.bdef()                           default = "loop" for colors, 0.45 for radii
-r.tdef()  			   default = 0.25 for bond/line thickness
+r.tdef()                           default = 0.25 for bond/line thickness
-r.ldef()  			   default = 0 fill
+r.ldef()                           default = 0 fill
 
   by default 100 types are assigned
   if atom/bond/tri/line has type > # defined properties, is an error
@@ -108,16 +119,10 @@ colors["nickname"] = [R,G,B]       set new RGB values from 0 to 255
 #   vizinfo = scene attributes
 #   xtrans,ytrans,ztrans = translation factors computed by Raster3d
 
-# Imports and external programs
-
-import sys, os, commands, re
-from vizinfo import vizinfo
-from math import fabs,atan,cos,sin
-
 try: from DEFAULTS import PIZZA_RENDER
 except: PIZZA_RENDER = "render"
 try: from DEFAULTS import PIZZA_LABEL3D
-except: PIZZA_LABEL3D = "label3d"
+except: PIZZA_LABEL3D = "render -labels"
 try: from DEFAULTS import PIZZA_DISPLAY
 except: PIZZA_DISPLAY = "display"
 
@@ -152,6 +157,8 @@ class raster:
     self.tdef()
     self.ldef()
 
+    os.environ["TMPDIR"] = "/tmp"
+
   # --------------------------------------------------------------------
 
   def bg(self,color):
@@ -222,7 +229,7 @@ class raster:
 
     self.xtrans = self.ytrans = self.ztrans = 0.0
     output = self.single(1,self.file,box,atoms,bonds,tris,lines)
-    print output
+    print(output)
     nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output)
     self.xtrans = float(nums[0][0])
     self.ytrans = float(nums[0][1])
@@ -297,16 +304,16 @@ class raster:
           self.scale = self.scale_start + \
                           fraction*(self.scale_stop - self.scale_start)
 
-	if n == nstart or self.panflag:
+        if n == nstart or self.panflag:
           self.xtrans = self.ytrans = self.ztrans = 0.0
-	  output = self.single(1,file,box,atoms,bonds,tris,lines)
+          output = self.single(1,file,box,atoms,bonds,tris,lines)
           nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output)
           self.xtrans = float(nums[0][0])
           self.ytrans = float(nums[0][1])
           self.ztrans = float(nums[0][2])
 
         self.single(0,file,box,atoms,bonds,tris,lines)
-        print time,
+        print(time, end=' ')
         sys.stdout.flush()
         i += 1
         n += 1
@@ -344,20 +351,20 @@ class raster:
           self.scale = self.scale_start + \
                           fraction*(self.scale_stop - self.scale_start)
 
-	if n == nstart or self.panflag:
+        if n == nstart or self.panflag:
           self.xtrans = self.ytrans = self.ztrans = 0.0
-	  output = self.single(1,file,box,atoms,bonds,tris,lines)
+          output = self.single(1,file,box,atoms,bonds,tris,lines)
           nums = re.findall("translation to:\s*(\S*)\s*(\S*)\s*(\S*)\s",output)
           self.xtrans = float(nums[0][0])
           self.ytrans = float(nums[0][1])
           self.ztrans = float(nums[0][2])
 
         self.single(0,file,box,atoms,bonds,tris,lines)
-        print n,
+        print(n, end=' ')
         sys.stdout.flush()
         n += 1
 
-    print "\n%d images" % ncount
+    print("\n%d images" % ncount)
 
   # --------------------------------------------------------------------
 
@@ -374,7 +381,7 @@ class raster:
              (self.xpixels,self.ypixels,color[0],color[1],color[2],
               self.eye,matrix,self.xtrans+xshift,self.ytrans+yshift,
               self.ztrans,1.6*self.distance/self.scale)
-    print >>f,header,
+    print(header, end=' ', file=f)
 
     # draw box if boxflag or flag is set
     # flag = 1 is a pre-call of single to set frame size correctly
@@ -385,53 +392,53 @@ class raster:
     ncolor = self.vizinfo.nacolor
     for atom in atoms:
       itype = int(atom[1])
-      if itype > ncolor: raise StandardError,"atom type too big"
+      if itype > ncolor: raise Exception("atom type too big")
       color = self.vizinfo.acolor[itype]
       rad = self.vizinfo.arad[itype]
-      print >>f,2
+      print(2, file=f)
-      print >>f,atom[2],atom[3],atom[4],rad,color[0],color[1],color[2]
+      print(atom[2],atom[3],atom[4],rad,color[0],color[1],color[2], file=f)
 
     # need to include vizinfo.tfill options
 
     ncolor = self.vizinfo.ntcolor
     for tri in tris:
       itype = int(tri[1])
-      if itype > ncolor: raise StandardError,"tri type too big"
+      if itype > ncolor: raise Exception("tri type too big")
       color = self.vizinfo.tcolor[itype]
-      print >>f,1
+      print(1, file=f)
-      print >>f,tri[2],tri[3],tri[4],tri[5],tri[6],tri[7], \
+      print(tri[2],tri[3],tri[4],tri[5],tri[6],tri[7], \
-            tri[8],tri[9],tri[10],color[0],color[1],color[2]
+            tri[8],tri[9],tri[10],color[0],color[1],color[2], file=f)
 
     bound = 0.25 * self.distance
     ncolor = self.vizinfo.nbcolor
     for bond in bonds:
       itype = int(bond[1])
-      if itype > ncolor: raise StandardError,"bond type too big"
+      if itype > ncolor: raise Exception("bond type too big")
       color = self.vizinfo.bcolor[itype]
       rad = self.vizinfo.brad[itype]
       if fabs(bond[2]-bond[5]) > bound or fabs(bond[3]-bond[6]) > bound:
         continue
-      print >>f,5
+      print(5, file=f)
-      print >>f,bond[2],bond[3],bond[4],rad, \
+      print(bond[2],bond[3],bond[4],rad, \
-            bond[5],bond[6],bond[7],0.0,color[0],color[1],color[2]
+            bond[5],bond[6],bond[7],0.0,color[0],color[1],color[2], file=f)
 
     ncolor = self.vizinfo.nlcolor
     for line in lines:
       itype = int(line[1])
-      if itype > ncolor: raise StandardError,"line type too big"
+      if itype > ncolor: raise Exception("line type too big")
       color = self.vizinfo.lcolor[itype]
       thick = self.vizinfo.lrad[itype]
-      print >>f,3  
+      print(3, file=f)
-      print >>f,line[2],line[3],line[4],thick, \
+      print(line[2],line[3],line[4],thick, \
-                line[5],line[6],line[7],thick,color[0],color[1],color[2]
+                line[5],line[6],line[7],thick,color[0],color[1],color[2], file=f)
 
     for label in self.labels:
-      print >>f,15
+      print(15, file=f)
-      print >>f,10
+      print(10, file=f)
-      print >>f,label[2],label[3],label[4]
+      print(label[2],label[3],label[4], file=f)
-      print >>f,11
+      print(11, file=f)
-      print >>f,label[0],label[1],0.0,label[5][0],label[5][1],label[5][2]
+      print(label[0],label[1],0.0,label[5][0],label[5][1],label[5][2], file=f)
-      print >>f,label[6]
+      print(label[6], file=f)
 
     f.close()
 
@@ -446,26 +453,26 @@ class raster:
   # --------------------------------------------------------------------
 
   def adef(self):
-    self.vizinfo.setcolors("atom",range(100),"loop")
+    self.vizinfo.setcolors("atom",list(range(100)),"loop")
-    self.vizinfo.setradii("atom",range(100),0.45)
+    self.vizinfo.setradii("atom",list(range(100)),0.45)
 
   # --------------------------------------------------------------------
 
   def bdef(self):
-    self.vizinfo.setcolors("bond",range(100),"loop")
+    self.vizinfo.setcolors("bond",list(range(100)),"loop")
-    self.vizinfo.setradii("bond",range(100),0.25)
+    self.vizinfo.setradii("bond",list(range(100)),0.25)
 
   # --------------------------------------------------------------------
 
   def tdef(self):
-    self.vizinfo.setcolors("tri",range(100),"loop")  
+    self.vizinfo.setcolors("tri",list(range(100)),"loop")
-    self.vizinfo.setfills("tri",range(100),0)  
+    self.vizinfo.setfills("tri",list(range(100)),0)
 
   # --------------------------------------------------------------------
 
   def ldef(self):
-    self.vizinfo.setcolors("line",range(100),"loop")  
+    self.vizinfo.setcolors("line",list(range(100)),"loop")
-    self.vizinfo.setradii("line",range(100),0.25)
+    self.vizinfo.setradii("line",list(range(100)),0.25)
 
   # --------------------------------------------------------------------
 
@@ -526,32 +533,32 @@ def box_write(f,box,color,thick):
   green = color[1]
   blue = color[2]
 
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-  	      (xlo,ylo,zlo,thick,xhi,ylo,zlo,thick,red,green,blue)
+              (xlo,ylo,zlo,thick,xhi,ylo,zlo,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,yhi,zlo,thick,xhi,yhi,zlo,thick,red,green,blue)
+              (xlo,yhi,zlo,thick,xhi,yhi,zlo,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,ylo,zhi,thick,xhi,ylo,zhi,thick,red,green,blue)
+              (xlo,ylo,zhi,thick,xhi,ylo,zhi,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,yhi,zhi,thick,xhi,yhi,zhi,thick,red,green,blue)
+              (xlo,yhi,zhi,thick,xhi,yhi,zhi,thick,red,green,blue), file=f)
 
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,ylo,zlo,thick,xlo,yhi,zlo,thick,red,green,blue)
+              (xlo,ylo,zlo,thick,xlo,yhi,zlo,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xhi,ylo,zlo,thick,xhi,yhi,zlo,thick,red,green,blue)
+              (xhi,ylo,zlo,thick,xhi,yhi,zlo,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,ylo,zhi,thick,xlo,yhi,zhi,thick,red,green,blue)
+              (xlo,ylo,zhi,thick,xlo,yhi,zhi,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xhi,ylo,zhi,thick,xhi,yhi,zhi,thick,red,green,blue)
+              (xhi,ylo,zhi,thick,xhi,yhi,zhi,thick,red,green,blue), file=f)
 
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,ylo,zlo,thick,xlo,ylo,zhi,thick,red,green,blue)
+              (xlo,ylo,zlo,thick,xlo,ylo,zhi,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xhi,ylo,zlo,thick,xhi,ylo,zhi,thick,red,green,blue)
+              (xhi,ylo,zlo,thick,xhi,ylo,zhi,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xlo,yhi,zlo,thick,xlo,yhi,zhi,thick,red,green,blue)
+              (xlo,yhi,zlo,thick,xlo,yhi,zhi,thick,red,green,blue), file=f)
-  print >>f,"3\n%g %g %g %g %g %g %g %g %g %g %g" % \
+  print("3\n%g %g %g %g %g %g %g %g %g %g %g" % \
-	      (xhi,yhi,zlo,thick,xhi,yhi,zhi,thick,red,green,blue)
+              (xhi,yhi,zlo,thick,xhi,yhi,zhi,thick,red,green,blue), file=f)
 
 # --------------------------------------------------------------------
 # compute 3x3 rotation matrix for viewing angle
@@ -634,7 +641,7 @@ def rotation_matrix(coord1,angle1,coord2,angle2):
   # each line padded with 0.0 for 4x4 raster3d matrix
 
   matrix = "%g %g %g 0.0\n%g %g %g 0.0\n%g %g %g 0.0" % \
-  	   (c11,c12,c13,c21,c22,c23,c31,c32,c33)
+           (c11,c12,c13,c21,c22,c23,c31,c32,c33)
   return matrix
 
 # --------------------------------------------------------------------

src/svg.py

@@ -8,6 +8,18 @@
 
 # svg tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, os, re
+try:
+  import commands
+except ImportError:
+  import subprocess as commands
+import functools
+from vizinfo import vizinfo
+from math import sqrt,atan,cos,sin,fabs
+
 oneline = "3d visualization via SVG files"
 
 docstr = """
@@ -16,8 +28,8 @@ s = svg(d)                  create SVG object for data in d
   d = atom snapshot object (dump, data)
 
 s.bg("black")               set background color (def = "black")
-s.size(N)		    set image size to NxN
+s.size(N)                   set image size to NxN
-s.size(N,M)		    set image size to NxM
+s.size(N,M)                 set image size to NxM
 s.rotate(60,135)            view from z theta and azimuthal phi (def = 60,30)
 s.shift(x,y)                translate by x,y pixels in view window (def = 0,0)
 s.zoom(0.5)                 scale image by factor (def = 1)
@@ -49,9 +61,9 @@ s.nolabel()                                      delete all labels
   x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font
   size = fontsize (e.g. 10), "red" = color of text
 
-s.acol(2,"green")		   set atom colors by atom type (1-N)
+s.acol(2,"green")                  set atom colors by atom type (1-N)
-s.acol([2,4],["red","blue"])	   1st arg = one type or list of types
+s.acol([2,4],["red","blue"])       1st arg = one type or list of types
-s.acol(0,"blue")          	   2nd arg = one color or list of colors
+s.acol(0,"blue")                   2nd arg = one color or list of colors
 s.acol(range(20),["red","blue"])   if list lengths unequal, interpolate
 s.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
@@ -61,19 +73,19 @@ s.acol(range(10),"loop")           assign colors in loop, randomly ordered
 
 s.arad([1,2],[0.5,0.3])            set atom radii, same rules as acol()
 
-s.bcol()			   set bond color, same args as acol()
+s.bcol()                           set bond color, same args as acol()
-s.brad()			   set bond thickness, same args as arad()
+s.brad()                           set bond thickness, same args as arad()
 
-s.tcol()			   set triangle color, same args as acol()
+s.tcol()                           set triangle color, same args as acol()
-s.tfill()			   set triangle fill, 0 fill, 1 line, 2 both
+s.tfill()                          set triangle fill, 0 fill, 1 line, 2 both
 
 s.lcol()                           set line color, same args as acol()
 s.lrad()                           set line thickness, same args as arad()
 
 s.adef()                           set atom/bond/tri/line properties to default
-s.bdef()			   default = "loop" for colors, 0.45 for radii
+s.bdef()                           default = "loop" for colors, 0.45 for radii
-s.tdef()  			   default = 0.25 for bond/line thickness
+s.tdef()                           default = 0.25 for bond/line thickness
-s.ldef()  			   default = 0 fill
+s.ldef()                           default = 0 fill
 
   by default 100 types are assigned
   if atom/bond/tri/line has type > # defined properties, is an error
@@ -110,12 +122,6 @@ s.thick = 2.0               pixel thickness of black atom border
 #   bgcol = color of background
 #   vizinfo = scene attributes
 
-# Imports and external programs
-
-import sys, os, commands, re
-from vizinfo import vizinfo
-from math import sqrt,atan,cos,sin,fabs
-
 try: from DEFAULTS import PIZZA_DISPLAY
 except: PIZZA_DISPLAY = "display"
 
@@ -248,10 +254,10 @@ class svg:
 
         fraction = float(i) / (ncount-1)
 
-	if self.select != "":
+        if self.select != "":
           newstr = self.select % fraction
           data.aselect.test(newstr,time)
-	time,boxone,atoms,bonds,tris,lines = data.viz(which)
+        time,boxone,atoms,bonds,tris,lines = data.viz(which)
 
         if self.boxflag < 2: box = boxone
         if n == nstart: self.distance = compute_distance(box)
@@ -261,7 +267,7 @@ class svg:
         elif n < 1000: file = self.file + "0" + str(n)
         else:          file = self.file + str(n)
 
-	if self.panflag:
+        if self.panflag:
           self.ztheta = self.ztheta_start + \
                         fraction*(self.ztheta_stop - self.ztheta_start)
           self.azphi = self.azphi_start + \
@@ -270,10 +276,10 @@ class svg:
                        fraction*(self.scale_stop - self.scale_start)
 
         scaleflag = 0
-	if n == nstart or self.panflag: scaleflag = 1       
+        if n == nstart or self.panflag: scaleflag = 1
 
-	self.single(file,box,atoms,bonds,tris,lines,scaleflag) 
+        self.single(file,box,atoms,bonds,tris,lines,scaleflag)
-        print time,
+        print(time, end=' ')
         sys.stdout.flush()
         i += 1
         n += 1
@@ -290,7 +296,7 @@ class svg:
       for i in range(ncount):
         fraction = float(i) / (ncount-1)
 
-	if self.select != "":
+        if self.select != "":
           newstr = self.select % fraction
           data.aselect.test(newstr,ntime)
         time,boxone,atoms,bonds,tris,lines = data.viz(which)
@@ -303,23 +309,23 @@ class svg:
         elif n < 1000: file = self.file + "0" + str(n)
         else:          file = self.file + str(n)
 
-	if self.panflag:
+        if self.panflag:
           self.ztheta = self.ztheta_start + \
                         fraction*(self.ztheta_stop - self.ztheta_start)
           self.azphi = self.azphi_start + \
                        fraction*(self.azphi_stop - self.azphi_start)
-	  self.scale = self.scale_start + \
+          self.scale = self.scale_start + \
                        fraction*(self.scale_stop - self.scale_start)
 
         scaleflag = 0
-	if n == nstart or self.panflag: scaleflag = 1
+        if n == nstart or self.panflag: scaleflag = 1
 
-	self.single(file,box,atoms,bonds,tris,lines,scaleflag) 
+        self.single(file,box,atoms,bonds,tris,lines,scaleflag)
-        print n,
+        print(n, end=' ')
         sys.stdout.flush()
         n += 1
 
-    print "\n%d images" % ncount  
+    print("\n%d images" % ncount)
 
   # --------------------------------------------------------------------
 
@@ -420,7 +426,7 @@ class svg:
     # convert objects by factor/offset and sort by z-depth
 
     self.convert(olist)
-    olist.sort(cmprz)
+    olist.sort(key = functools.cmp_to_key(cmprz))
 
     # write SVG file
 
@@ -430,19 +436,19 @@ class svg:
     header = '<?xml version="1.0"?> <svg height="%s" width="%s" >' % \
              (self.ypixels,self.xpixels)
     header += '<g style="fill-opacity:1.0; stroke:black; stroke-width:0.001;">'
-    print >>f,header
+    print(header, file=f)
 
     color = '<rect x="0" y="0" height="%s" width="%s" ' % \
             (self.ypixels,self.xpixels)
     color += 'fill="rgb(%s,%s,%s)"/>' % \
              (self.bgcol[0]*255,self.bgcol[1]*255,self.bgcol[2]*255)
-    print >>f,color
+    print(color, file=f)
 
     for element in olist: self.write(f,0,element)
     for label in self.labels: self.write(f,1,label)
 
     footer = "</g></svg>"
-    print >> f,footer 
+    print(footer, file=f)
 
     f.close()
 
@@ -512,82 +518,82 @@ class svg:
 
     if flag == 0:
       if obj[0] == 0:     # atom with its color and radius
-	itype = int(obj[1])
+        itype = int(obj[1])
-	if itype > self.vizinfo.nacolor:
+        if itype > self.vizinfo.nacolor:
-          raise StandardError,"atom type too big"
+          raise Exception("atom type too big")
         color = self.vizinfo.acolor[itype]
         rad = self.vizinfo.arad[itype]
-	print >>f,'<circle cx="%s" cy="%s" r="%s" fill="rgb(%s,%s,%s)" stroke-width="%s" />' % \
+        print('<circle cx="%s" cy="%s" r="%s" fill="rgb(%s,%s,%s)" stroke-width="%s" />' % \
                    (obj[2],obj[3],rad*self.factor,
-                    color[0]*255,color[1]*255,color[2]*255,self.thick)
+                    color[0]*255,color[1]*255,color[2]*255,self.thick), file=f)
 
       elif obj[0] == 1:    # tri with its color (need to add fill type)
         itype = int(obj[1])
-	if itype > self.vizinfo.ntcolor:
+        if itype > self.vizinfo.ntcolor:
-          raise StandardError,"tri type too big"
+          raise Exception("tri type too big")
         color = self.vizinfo.tcolor[itype]
-        print >>f,'<polygon points= "%s,%s %s,%s %s,%s" fill="rgb(%s,%s,%s)" stroke="black" stroke-width="0.01" />' % \
+        print('<polygon points= "%s,%s %s,%s %s,%s" fill="rgb(%s,%s,%s)" stroke="black" stroke-width="0.01" />' % \
               (obj[2],obj[3],obj[5],obj[6],obj[8],obj[9],
-               color[0]*255,color[1]*255,color[2]*255)
+               color[0]*255,color[1]*255,color[2]*255), file=f)
 
       elif obj[0] == 2:    # bond with its color and thickness
         itype = int(obj[1])
-	if itype > self.vizinfo.nbcolor:
+        if itype > self.vizinfo.nbcolor:
-          raise StandardError,"bond type too big"
+          raise Exception("bond type too big")
         color = self.vizinfo.bcolor[itype]
         thick = self.vizinfo.brad[itype]
-	print >>f,'<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
+        print('<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
               (obj[2],obj[3],obj[5],obj[6],
-               color[0]*255,color[1]*255,color[2]*255,thick*self.factor)
+               color[0]*255,color[1]*255,color[2]*255,thick*self.factor), file=f)
 
       elif obj[0] == 3:    # line with its color and thickness
         itype = int(obj[1])
-	if itype > self.vizinfo.nlcolor:
+        if itype > self.vizinfo.nlcolor:
-          raise StandardError,"line type too big"
+          raise Exception("line type too big")
         color = self.vizinfo.lcolor[itype]
         thick = self.vizinfo.lrad[itype]
-        print >>f,'<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
+        print('<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
               (obj[2],obj[3],obj[5],obj[6],
-               color[0]*255,color[1]*255,color[2]*255,thick*self.factor)
+               color[0]*255,color[1]*255,color[2]*255,thick*self.factor), file=f)
 
       elif obj[0] == 4:    # box line with built-in color and thickness
         color = self.bxcol
         thick = self.bxthick
-        print >>f,'<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
+        print('<line x1="%s" y1="%s" x2="%s" y2="%s" stroke="rgb(%s,%s,%s)" stroke-width="%s" />' % \
               (obj[2],obj[3],obj[5],obj[6],
-               color[0]*255,color[1]*255,color[2]*255,thick*self.factor)
+               color[0]*255,color[1]*255,color[2]*255,thick*self.factor), file=f)
 
     elif flag == 1:
       x = (obj[0]*self.xpixels) + (self.xpixels/2.0)
       y = (self.ypixels/2.0) - (obj[1]*self.ypixels)
       color = obj[4]
-      print >>f,'<text x="%s" y="%s" font-size="%s" font-family="%s" stroke="rgb(%s,%s,%s)" fill="rgb(%s,%s,%s"> %s </text>' % \
+      print('<text x="%s" y="%s" font-size="%s" font-family="%s" stroke="rgb(%s,%s,%s)" fill="rgb(%s,%s,%s"> %s </text>' % \
               (x,y,obj[3],obj[2],color[0]*255,color[1]*255,color[2]*255,
-               color[0]*255,color[1]*255,color[2]*255,obj[5])
+               color[0]*255,color[1]*255,color[2]*255,obj[5]), file=f)
 
   # --------------------------------------------------------------------
 
   def adef(self):
-    self.vizinfo.setcolors("atom",range(100),"loop")
+    self.vizinfo.setcolors("atom",list(range(100)),"loop")
-    self.vizinfo.setradii("atom",range(100),0.45)
+    self.vizinfo.setradii("atom",list(range(100)),0.45)
 
   # --------------------------------------------------------------------
 
   def bdef(self):
-    self.vizinfo.setcolors("bond",range(100),"loop")
+    self.vizinfo.setcolors("bond",list(range(100)),"loop")
-    self.vizinfo.setradii("bond",range(100),0.25)
+    self.vizinfo.setradii("bond",list(range(100)),0.25)
 
   # --------------------------------------------------------------------
 
   def tdef(self):
-    self.vizinfo.setcolors("tri",range(100),"loop")  
+    self.vizinfo.setcolors("tri",list(range(100)),"loop")
-    self.vizinfo.setfills("tri",range(100),0)  
+    self.vizinfo.setfills("tri",list(range(100)),0)
 
   # --------------------------------------------------------------------
 
   def ldef(self):
-    self.vizinfo.setcolors("line",range(100),"loop")  
+    self.vizinfo.setcolors("line",list(range(100)),"loop")
-    self.vizinfo.setradii("line",range(100),0.25)
+    self.vizinfo.setradii("line",list(range(100)),0.25)
 
   # --------------------------------------------------------------------
 

src/tdump.py

@@ -8,18 +8,26 @@
 
 # tdump tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys, re, glob, types
+import functools
+from math import sqrt
+from os import popen
+
 oneline = "Read dump files with triangle info"
 
 docstr = """
 t = tdump("dump.one")             read in one or more dump files
-t = tdump("dump.1 dump.2.gz")	  can be gzipped
+t = tdump("dump.1 dump.2.gz")     can be gzipped
-t = tdump("dump.*")		  wildcard expands to multiple files
+t = tdump("dump.*")               wildcard expands to multiple files
-t = tdump("dump.*",0)		  two args = store filenames, but don't read
+t = tdump("dump.*",0)             two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
   no column name assignment is performed
 
-time = t.next()             	  read next snapshot from dump files
+time = t.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -43,7 +51,7 @@ time,box,atoms,bonds,tris,lines = t.viz(index)   return list of viz objects
       id,type are from associated atom
     lines = NULL
 
-t.owrap(...)		          wrap tris to same image as their atoms
+t.owrap(...)                      wrap tris to same image as their atoms
 
   owrap() is called by dump tool's owrap()
   useful for wrapping all molecule's atoms/tris the same so it is contiguous
@@ -67,12 +75,6 @@ t.owrap(...)		          wrap tris to same image as their atoms
 #     xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
-# Imports and external programs
-
-import sys, commands, re, glob, types
-from math import sqrt
-from os import popen
-
 try:
     import numpy as np
     oldnumeric = False
@@ -100,7 +102,7 @@ class tdump:
     self.flist = []
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
-      raise StandardError,"no ldump file specified"
+      raise Exception("no ldump file specified")
 
     if len(list) == 1:
       self.increment = 0
@@ -125,26 +127,26 @@ class tdump:
       snap = self.read_snapshot(f)
       while snap:
         self.snaps.append(snap)
-        print snap.time,
+        print(snap.time, end=' ')
         sys.stdout.flush()
         snap = self.read_snapshot(f)
 
       f.close()
-    print
+    print()
 
     # sort entries by timestep, cull duplicates
 
-    self.snaps.sort(self.compare_time)
+    self.snaps.sort(key = functools.cmp_to_key(self.compare_time))
     self.cull()
     self.nsnaps = len(self.snaps)
-    print "read %d snapshots" % self.nsnaps
+    print("read %d snapshots" % self.nsnaps)
 
   # --------------------------------------------------------------------
   # read next snapshot from list of files
 
   def next(self):
 
-    if not self.increment: raise StandardError,"cannot read incrementally"
+    if not self.increment: raise Exception("cannot read incrementally")
 
     # read next snapshot in current file using eof as pointer
     # if fail, try next file
@@ -156,15 +158,15 @@ class tdump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
+        self.eof = 0
-	continue
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     self.snaps.append(snap)
@@ -198,14 +200,14 @@ class tdump:
       if snap.natoms:
         words = f.readline().split()
         ncol = len(words)
-        for i in xrange(1,snap.natoms):
+        for i in range(1,snap.natoms):
           words += f.readline().split()
-        floats = map(float,words)
+        floats = list(map(float,words))
         if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
         else: atoms = np.zeros((snap.natoms,ncol),np.float)
         start = 0
         stop = ncol
-        for i in xrange(snap.natoms):
+        for i in range(snap.natoms):
           atoms[i] = floats[start:stop]
           start = stop
           stop += ncol
@@ -220,7 +222,7 @@ class tdump:
 
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
-      raise StandardError, "tdump map() requires pairs of mappings"
+      raise Exception("tdump map() requires pairs of mappings")
     for i in range(0,len(pairs),2):
       j = i + 1
       self.names[pairs[j]] = pairs[i]-1
@@ -250,9 +252,9 @@ class tdump:
   # --------------------------------------------------------------------
 
   def findtime(self,n):
-    for i in xrange(self.nsnaps):
+    for i in range(self.nsnaps):
       if self.snaps[i].time == n: return i
-    raise StandardError, "no step %d exists" % n
+    raise Exception("no step %d exists" % n)
 
   # --------------------------------------------------------------------
   # delete successive snapshots with duplicate time stamp
@@ -295,11 +297,11 @@ class tdump:
     corner3y = self.names["corner3y"]
     corner3z = self.names["corner3z"]
 
-    # create line list from id,type,corner1x,...corner3z
+    # create tris list from id,type,corner1x,...corner3z
-    # don't add line if all 4 values are 0 since not a line
+    # don't add tri if all 4 values are 0 since not a line
 
     tris = []
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       atom = snap.atoms[i]
       c1 = [atom[corner1x],atom[corner1y],atom[corner1z]]
       c2 = [atom[corner2x],atom[corner2y],atom[corner2z]]
@@ -335,7 +337,7 @@ class tdump:
     # jdump = atom J in dump's atoms that atom I was owrapped on
     # delx,dely = offset applied to atom I and thus to line I
 
-    for i in xrange(snap.natoms):
+    for i in range(snap.natoms):
       tag = atoms[i][id]
       idump = idsdump[tag]
       jdump = idsdump[atomsdump[idump][iother]]

src/vcr.py

@@ -8,6 +8,15 @@
 
 # vcr tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+try:
+  from Tkinter import *
+except ImportError:
+  from tkinter import *
+import types
+
 oneline = "VCR-style GUI for 3d interactive OpenGL visualization"
 
 docstr = """
@@ -16,26 +25,26 @@ v.add(gl)                  add a gl window to vcr GUI
 
 Actions (same as GUI widgets):
 
-v.first()		   go to first frame
+v.first()                  go to first frame
 v.prev()                   go to previous frame
 v.back()                   play backwards from current frame to start
-v.stop()         	   stop on current frame		
+v.stop()                   stop on current frame
 v.play()                   play from current frame to end
-v.next()		   go to next frame
+v.next()                   go to next frame
-v.last()		   go to last frame
+v.last()                   go to last frame
 
-v.frame(31)    	           set frame slider
+v.frame(31)                set frame slider
-v.delay(0.4)     	   set delay slider
+v.delay(0.4)               set delay slider
-v.q(5)          	   set quality slider
+v.q(5)                     set quality slider
 
-v.xaxis()		   view scene from x axis
+v.xaxis()                  view scene from x axis
-v.yaxis()  		   view scene from y axis
+v.yaxis()                  view scene from y axis
-v.zaxis()		   view scene from z axis
+v.zaxis()                  view scene from z axis
-v.box()		 	   toggle bounding box
+v.box()                    toggle bounding box
-v.axis() 	           toggle display of xyz axes
+v.axis()                   toggle display of xyz axes
-v.norm()	           recenter and resize the view
+v.norm()                   recenter and resize the view
-v.ortho()	           toggle ortho/perspective button
+v.ortho()                  toggle ortho/perspective button
-v.reload()           	   reload all frames from gl viewer data files
+v.reload()                 reload all frames from gl viewer data files
 
 v.clipxlo(0.2)             clip scene at x lo fraction of box
 v.clipxhi(1.0)             clip at x hi
@@ -44,9 +53,9 @@ v.clipyhi(1.0)
 v.clipzlo(0.2)             clip in z
 v.clipzhi(1.0)
 
-v.save()		   save current scene to file.png
+v.save()                   save current scene to file.png
-v.file("image")		   set filename
+v.file("image")            set filename
-v.saveall()		   toggle save-all checkbox
+v.saveall()                toggle save-all checkbox
 """
 
 # History
@@ -64,11 +73,6 @@ v.saveall()		   toggle save-all checkbox
 #   delay_value = delay between frames (secs)
 #   delay_msec = delay in millisec
 
-# Imports and external programs
-
-from Tkinter import *
-import types
-
 # Class definition
 
 class vcr:
@@ -88,7 +92,7 @@ class vcr:
     # load data for each viewer
     # if each viewer has different data set, nframes is for 1st viewer
 
-    if len(views) == 0: raise StandardError,"must have at least one GL viewer"
+    if len(views) == 0: raise Exception("must have at least one GL viewer")
     self.viewlist = []
     for view in views: self.viewlist.append(view)
     for view in self.viewlist: view.reload()
@@ -320,7 +324,7 @@ class vcr:
   # --------------------------------------------------------------------
 
   def q(self,value):
-    if type(value) is not types.IntType: value = self.slider_quality.get()
+    if type(value) is not int: value = self.slider_quality.get()
     self.slider_quality.set(value)
     for view in self.viewlist: view.q(value)
 

src/vec.py

@@ -8,6 +8,11 @@
 
 # vec tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import types
+
 oneline = "Create numeric vectors from columns in file or list of vecs"
 
 docstr = """
@@ -19,10 +24,10 @@ v = vec(array)                      array = list of numeric vectors
   assigns names = "col1", "col2", etc
 
 nvec = v.nvec                       # of vectors
-nlen = v.nlen		            lengths of vectors
+nlen = v.nlen                       lengths of vectors
-names = v.names		            list of vector names
+names = v.names                     list of vector names
 x,y,... = l.get(1,"col2",...)       return one or more vectors of values
-l.write("file.txt")	            write all vectors to a file
+l.write("file.txt")                 write all vectors to a file
 l.write("file.txt","col1",7,...)    write listed vectors to a file
 
   get and write allow abbreviated (uniquely) vector names or digits (1-Nvec)
@@ -40,10 +45,6 @@ l.write("file.txt","col1",7,...)    write listed vectors to a file
 #   ptr = dictionary, key = name, value = index into data for which column
 #   data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1
 
-# Imports and external programs
-
-import types
-
 # Class definition
 
 class vec:
@@ -53,22 +54,22 @@ class vec:
   def __init__(self,data):
     self.data = []
 
-    if type(data) == types.StringType:
+    if isinstance(data,str):
       lines = open(data,'r').readlines()
       for line in lines:
         words = line.split()
         if len(words) and words[0][0] in "0123456789.-":
-          self.data.append(map(float,words))
+          self.data.append(list(map(float,words)))
-    elif type(data) == types.ListType:
+    elif isinstance(data, list):
       nlen = len(data[0])
-      for list in data[1:]:
+      for dlist in data[1:]:
-        if len(list) != nlen:
+        if len(dlist) != nlen:
-          raise StandardError,"lists are not all same length"
+          raise Exception("lists are not all same length")
-      for i in xrange(nlen):
+      for i in range(nlen):
-        values = [list[i] for list in data]
+        values = [dlist[i] for dlist in data]
-        self.data.append(map(float,values))
+        self.data.append(list(map(float,values)))
     else:
-      raise StandardError,"invalid argument to vec"
+      raise Exception("invalid argument to vec")
 
     if len(self.data) == 0:
       self.nlen = self.nvec = 0
@@ -77,40 +78,40 @@ class vec:
       self.nvec = len(self.data[0])
 
     self.names = []
-    for i in xrange(self.nvec):
+    for i in range(self.nvec):
       self.names.append(str("col%d" % (i+1)))
 
     self.ptr = {}
-    for i in xrange(self.nvec):
+    for i in range(self.nvec):
       self.ptr[self.names[i]] = i
 
-    print "read %d vectors of length %d" % (self.nvec,self.nlen)
+    print("read %d vectors of length %d" % (self.nvec,self.nlen))
 
   # --------------------------------------------------------------------
 
   def get(self,*keys):
     if len(keys) == 0:
-      raise StandardError, "no vectors specified"
+      raise Exception("no vectors specified")
 
     map = []
     for key in keys:
-      if type(key) == types.IntType: map.append(key-1)
+      if type(key) == int: map.append(key-1)
-      elif self.ptr.has_key(key): map.append(self.ptr[key])
+      elif key in self.ptr: map.append(self.ptr[key])
       else:
         count = 0
         for i in range(self.nvec):
-	  if self.names[i].find(key) == 0:
+          if self.names[i].find(key) == 0:
-	    count += 1
+            count += 1
-	    index = i
+            index = i
         if count == 1:
           map.append(index)
         else:
-          raise StandardError, "unique vector %s not found" % key
+          raise Exception("unique vector %s not found" % key)
 
     vecs = []
     for i in range(len(keys)):
       vecs.append(self.nlen * [0])
-      for j in xrange(self.nlen):
+      for j in range(self.nlen):
         vecs[i][j] = self.data[j][map[i]]
 
     if len(keys) == 1: return vecs[0]
@@ -122,24 +123,24 @@ class vec:
     if len(keys):
       map = []
       for key in keys:
-        if type(key) == types.IntType: map.append(key-1)
+        if type(key) == int: map.append(key-1)
-        elif self.ptr.has_key(key): map.append(self.ptr[key])
+        elif key in self.ptr: map.append(self.ptr[key])
         else:
           count = 0
           for i in range(self.nvec):
-	    if self.names[i].find(key) == 0:
+            if self.names[i].find(key) == 0:
-	      count += 1
+              count += 1
-	      index = i
+              index = i
           if count == 1:
             map.append(index)
           else:
-            raise StandardError, "unique vector %s not found" % key
+            raise Exception("unique vector %s not found" % key)
     else:
-      map = range(self.nvec)
+      map = list(range(self.nvec))
 
     f = open(filename,"w")
-    for i in xrange(self.nlen):
+    for i in range(self.nlen):
-      for j in xrange(len(map)):
+      for j in range(len(map)):
-        print >>f,self.data[i][map[j]],
+        print(self.data[i][map[j]], end=' ', file=f)
-      print >>f
+      print(file=f)
     f.close()

src/vizinfo.py

@@ -18,6 +18,7 @@
 
 # Imports and external programs
 
+from __future__ import print_function, absolute_import
 import types
 
 # Class definition
@@ -66,20 +67,20 @@ class vizinfo:
     # convert args into lists if single values
     # if arg = 0, convert to full-range list
 
-    if type(ids) is types.IntType and ids == 0:
+    if type(ids) is int and ids == 0:
-      if which == "atom": ids = range(self.nacolor)
+      if which == "atom": ids = list(range(self.nacolor))
-      if which == "bond": ids = range(self.nbcolor)
+      if which == "bond": ids = list(range(self.nbcolor))
-      if which == "tri": ids = range(self.ntcolor)
+      if which == "tri": ids = list(range(self.ntcolor))
-      if which == "line": ids = range(self.nlcolor)
+      if which == "line": ids = list(range(self.nlcolor))
-    if type(ids) is not types.ListType and type(ids) is not types.TupleType:
+    if type(ids) is not list and type(ids) is not tuple:
       ids = [ids]
-    if type(rgbs) is not types.ListType and type(rgbs) is not types.TupleType:
+    if type(rgbs) is not list and type(rgbs) is not tuple:
       rgbs = [rgbs]
 
     # 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
@@ -109,12 +110,12 @@ 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":
-        list = colors.keys()
+        colorlist = list(colors.keys())
-        red,green,blue = colors[list[i % len(colors)]]
+        red,green,blue = colors[colorlist[i % len(colors)]]
       elif ntypes == nrgbs:
         red,green,blue = colors[rgbs[i]]
       else:
@@ -144,20 +145,20 @@ class vizinfo:
     # convert args into lists if single values
     # if arg = 0, convert to full-range list
 
-    if type(ids) is types.IntType and ids == 0:
+    if type(ids) is int and ids == 0:
-      if which == "atom": ids = range(self.narad)
+      if which == "atom": ids = list(range(self.narad))
-      if which == "bond": ids = range(self.nbrad)
+      if which == "bond": ids = list(range(self.nbrad))
-      if which == "line": ids = range(self.nlrad)
+      if which == "line": ids = list(range(self.nlrad))
-    if type(ids) is not types.ListType and type(ids) is not types.TupleType:
+    if type(ids) is not list and type(ids) is not tuple:
       ids = [ids]
-    if type(radii) is not types.ListType and \
+    if type(radii) is not list and \
-           type(radii) is not types.TupleType:
+           type(radii) is not tuple:
       radii = [radii]
 
     # 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
@@ -209,18 +210,18 @@ class vizinfo:
     # convert args into lists if single values
     # if arg = 0, convert to full-range list
 
-    if type(ids) is types.IntType and ids == 0:
+    if type(ids) is int and ids == 0:
-      ids = range(self.ntfill)
+      ids = list(range(self.ntfill))
-    if type(ids) is not types.ListType and type(ids) is not types.TupleType:
+    if type(ids) is not list and type(ids) is not tuple:
       ids = [ids]
-    if type(fills) is not types.ListType and \
+    if type(fills) is not list and \
-           type(fills) is not types.TupleType:
+           type(fills) is not tuple:
       fills = [fills]
 
     # 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 +235,7 @@ 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])
 

src/vmd.py

@@ -14,37 +14,38 @@
 #   open a pipe to the executable,
 #   and feed it Tcl command lines one at a time
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import types, os
+import numpy
+
 oneline = "Control VMD from python"
 
 docstr = """
-v = vmd()		       start up VMD
+v = vmd()                      start up VMD
-v.stop()		       shut down VMD instance
+v.stop()                       shut down VMD instance
-v.clear()		       delete all visualizations
+v.clear()                      delete all visualizations
 
-v.rep(style)		       set default representation style. One of
+v.rep(style)                   set default representation style. One of
-			       (Lines|VDW|Licorice|DynamicBonds|Points|CPK) 
+                               (Lines|VDW|Licorice|DynamicBonds|Points|CPK)
-v.new(file[,type])   	       load new file (default file type 'lammpstrj')
+v.new(file[,type])             load new file (default file type 'lammpstrj')
 v.data(file[,atomstyle])       load new data file (default atom style 'full')
-v.replace(file[,type])	       replace current frames with new file
+v.replace(file[,type])         replace current frames with new file
-v.append(file[,type]) 	       append file to current frame(s)
+v.append(file[,type])          append file to current frame(s)
 v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
 
-v.frame(frame)		       set current frame
+v.frame(frame)                 set current frame
-v.flush()		       flush pending input to VMD and update GUI
+v.flush()                      flush pending input to VMD and update GUI
-v.read(file)		       read Tcl script file (e.g. saved state)
+v.read(file)                   read Tcl script file (e.g. saved state)
 
-v.enter()		       enter interactive shell
+v.enter()                      enter interactive shell
-v.debug([True|False])	       display generated VMD script commands?
+v.debug([True|False])          display generated VMD script commands?
 """
 
 # History
 #   11/10, Axel Kohlmeyer (Temple U): original version
 
-# Imports and external programs
-
-import types, os
-import numpy
-
 try: from DEFAULTS import PIZZA_VMDNAME
 except: PIZZA_VMDNAME = "vmd"
 try: from DEFAULTS import PIZZA_VMDDIR
@@ -56,8 +57,8 @@ except: PIZZA_VMDARCH = "LINUX"
 
 try: import pexpect
 except:
-  print "pexpect from http://pypi.python.org/pypi/pexpect", \
+  print("pexpect from http://pypi.python.org/pypi/pexpect", \
-      "is required for vmd tool"
+      "is required for vmd tool")
   raise
 
 # Class definition
@@ -103,7 +104,7 @@ class vmd:
       self.VMD.sendline(command)
       self.VMD.expect('vmd >')
       if self.debugme:
-        print "call+result:"+self.VMD.before
+        print("call+result:"+self.VMD.before)
     return
 
   # --------------------------------------------------------------------
@@ -121,9 +122,9 @@ class vmd:
   # turn on debugging info
   def debug(self,status=True):
     if status and not self.debugme:
-      print 'Turning vmd.py debugging ON.'
+      print('Turning vmd.py debugging ON.')
     if not status and self.debugme:
-      print 'Turning vmd.py debugging OFF.'
+      print('Turning vmd.py debugging OFF.')
     self.debugme = status
 
   # --------------------------------------------------------------------
@@ -133,16 +134,16 @@ class vmd:
     self.__call__('menu main on')
     while 1:
       try:
-        command = raw_input("vmd > ")
+        command = input("vmd > ")
       except EOFError:
-        print "(EOF)"
+        print("(EOF)")
         self.__call__('menu main off')
         return
       if command == "quit" or command == "exit":
         self.__call__('menu main off')
         return
       if command == "gopython":
-        print "gopython not supported here"
+        print("gopython not supported here")
         continue
       self.__call__(command)
 

src/vtk.py

@@ -8,10 +8,13 @@
 
 # vtk tool
 
+from __future__ import print_function, absolute_import
+import sys, re
+
 oneline = "Convert LAMMPS snapshots to VTK format"
 
 docstr = """
-v = vtk(d)	        d = object containing atom coords (dump, data)
+v = vtk(d)              d = object containing atom coords (dump, data)
 
 v.one()                 write all snapshots to tmp.vtk
 v.one("new")            write all snapshots to new.vtk
@@ -34,8 +37,6 @@ v.single(N,"file")      write snapshot for timestep N to file.vtk
 
 # Imports and external programs
 
-import sys, re
-
 # Class definition
 
 class vtk:
@@ -55,7 +56,7 @@ class vtk:
     n = flag = 0
     which,time,flag = self.data.iterator(flag)
     time,box,atoms,bonds,tris,lines = self.data.viz(which)
-    print time,
+    print(time, end=' ')
     sys.stdout.flush()
 
     if len(tris): surface(tris)
@@ -70,12 +71,12 @@ class vtk:
       time,box,atoms,bonds,tris,lines = self.data.viz(which)
 
       for atom in atoms: allatoms.append(atom)
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
     particle(file,allatoms)
-    print "\nwrote %d snapshots to %s in VTK format" % (n,file)
+    print("\nwrote %d snapshots to %s in VTK format" % (n,file))
 
   # --------------------------------------------------------------------
 
@@ -105,11 +106,11 @@ class vtk:
 
       particle(file,atoms)
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
-    print "\nwrote %s snapshots in VTK format" % n
+    print("\nwrote %s snapshots in VTK format" % n)
   # --------------------------------------------------------------------
   def manyGran(self,*args,**kwargs):
 
@@ -159,11 +160,11 @@ class vtk:
       except: nvalues = 0
       particleGran(file,atoms,names,nvalues)
 
-      if outputfl: print time,
+      if outputfl: print(time, end=' ')
       if outputfl: sys.stdout.flush()
       n += 1
 
-    if outputfl: print "\nwrote %s granular snapshots in VTK format" % n
+    if outputfl: print("\nwrote %s granular snapshots in VTK format" % n)
   # --------------------------------------------------------------------
 
   def single(self,time,*args):
@@ -210,7 +211,7 @@ def generateFilename(root,fileNos,n):
 def surface(tris):
   ntypes = tris[-1][1]
 
-  for i in xrange(ntypes):
+  for i in range(ntypes):
     itype = i+1
     v = {}
     nvert = ntri = 0
@@ -218,19 +219,19 @@ def surface(tris):
       if tri[1] == itype:
         ntri += 1
         vert = (tri[2],tri[3],tri[4])
-        if not v.has_key(vert):
+        if vert not in v:
           v[vert] = nvert
           nvert += 1
         vert = (tri[5],tri[6],tri[7])
-        if not v.has_key(vert):
+        if vert not in v:
           v[vert] = nvert
           nvert += 1
         vert = (tri[8],tri[9],tri[10])
-        if not v.has_key(vert):
+        if vert not in v:
           v[vert] = nvert
           nvert += 1
 
-    keys = v.keys()
+    keys = list(v.keys())
     vinverse = {}
     for key in keys:
       vinverse[v[key]] = key
@@ -238,15 +239,15 @@ def surface(tris):
     filename = "SURF" + str(itype) + ".vtk"
     f = open(filename,"w")
 
-    print >>f,"# vtk DataFile Version 3.0"
+    print("# vtk DataFile Version 3.0", file=f)
-    print >>f,"Generated by pizza.py"
+    print("Generated by pizza.py", file=f)
-    print >>f,"ASCII"
+    print("ASCII", file=f)
-    print >>f,"DATASET POLYDATA"
+    print("DATASET POLYDATA", file=f)
-    print >>f,"POINTS %d float" % nvert
+    print("POINTS %d float" % nvert, file=f)
-    for i in xrange(nvert):
+    for i in range(nvert):
       tuple = vinverse[i]
-      print >>f,tuple[0],tuple[1],tuple[2]
+      print(tuple[0],tuple[1],tuple[2], file=f)
-    print >>f,"POLYGONS",ntri,4*ntri
+    print("POLYGONS",ntri,4*ntri, file=f)
     for tri in tris:
       if tri[1] == itype:
         vert = (tri[2],tri[3],tri[4])
@@ -255,10 +256,10 @@ def surface(tris):
         ivert2 = v[vert]
         vert = (tri[8],tri[9],tri[10])
         ivert3 = v[vert]
-        print >>f,3,ivert1,ivert2,ivert3
+        print(3,ivert1,ivert2,ivert3, file=f)
-    print >>f
+    print(file=f)
-    print >>f,"CELL_DATA",ntri
+    print("CELL_DATA",ntri, file=f)
-    print >>f,"POINT_DATA",nvert
+    print("POINT_DATA",nvert, file=f)
 
     f.close()
 
@@ -268,23 +269,23 @@ def surface(tris):
 def particle(file,atoms):
   f = open(file,"w")
 
-  print >>f,"# vtk DataFile Version 2.0"
+  print("# vtk DataFile Version 2.0", file=f)
-  print >>f,"Generated by pizza.py"
+  print("Generated by pizza.py", file=f)
-  print >>f,"ASCII"
+  print("ASCII", file=f)
-  print >>f,"DATASET POLYDATA"
+  print("DATASET POLYDATA", file=f)
-  print >>f,"POINTS %d float" % len(atoms)
+  print("POINTS %d float" % len(atoms), file=f)
   for atom in atoms:
-    print >>f,atom[2],atom[3],atom[4]
+    print(atom[2],atom[3],atom[4], file=f)
-  print >>f,"VERTICES",len(atoms),2*len(atoms)
+  print("VERTICES",len(atoms),2*len(atoms), file=f)
-  for i in xrange(len(atoms)):
+  for i in range(len(atoms)):
-    print >>f,1,i
+    print(1,i, file=f)
-  print >>f,"POINT_DATA",len(atoms)
+  print("POINT_DATA",len(atoms), file=f)
-  print >>f,"SCALARS atom_type int 1"
+  print("SCALARS atom_type int 1", file=f)
-  print >>f,"LOOKUP_TABLE default"
+  print("LOOKUP_TABLE default", file=f)
   for atom in atoms:
     itype = int(atom[1])
-    print >>f,itype,
+    print(itype, end=' ', file=f)
-  print >>f
+  print(file=f)
 
   f.close()
 
@@ -292,17 +293,17 @@ def particle(file,atoms):
 def boundingBox(file,xlo,xhi,ylo,yhi,zlo,zhi):
   f = open(file,"w")
 
-  print >>f,"# vtk DataFile Version 2.0"
+  print("# vtk DataFile Version 2.0", file=f)
-  print >>f,"Generated by pizza.py"
+  print("Generated by pizza.py", file=f)
-  print >>f,"ASCII"
+  print("ASCII", file=f)
-  print >>f,"DATASET RECTILINEAR_GRID"
+  print("DATASET RECTILINEAR_GRID", file=f)
-  print >>f,"DIMENSIONS 2 2 2"  
+  print("DIMENSIONS 2 2 2", file=f)
-  print >>f,"X_COORDINATES 2 float"
+  print("X_COORDINATES 2 float", file=f)
-  print >>f,xlo,xhi
+  print(xlo,xhi, file=f)
-  print >>f,"Y_COORDINATES 2 float"
+  print("Y_COORDINATES 2 float", file=f)
-  print >>f,ylo,yhi  
+  print(ylo,yhi, file=f)
-  print >>f,"Z_COORDINATES 2 float"
+  print("Z_COORDINATES 2 float", file=f)
-  print >>f,zlo,zhi
+  print(zlo,zhi, file=f)
 
 def typestr(o):
   string = str(type(o))
@@ -320,20 +321,20 @@ def particleGran(file,atoms,names,n_values):
   scalars, vectors = findScalarsAndVectors(names)
 
   # print head
-  print >>f,"# vtk DataFile Version 2.0"
+  print("# vtk DataFile Version 2.0", file=f)
-  print >>f,"Generated by lpp.py"
+  print("Generated by lpp.py", file=f)
-  print >>f,"ASCII"
+  print("ASCII", file=f)
-  print >>f,"DATASET POLYDATA"
+  print("DATASET POLYDATA", file=f)
-  print >>f,"POINTS %d float" % len(atoms)
+  print("POINTS %d float" % len(atoms), file=f)
   for atom in atoms:
-    print >>f, atom[vectors['x']], atom[vectors['x']+1], atom[vectors['x']+2] #atom[3],atom[4],atom[5]  #write x,y,z  [atom[0]=id, atom[1]=type]
+    print(atom[vectors['x']], atom[vectors['x']+1], atom[vectors['x']+2] , file=f) #atom[3],atom[4],atom[5]  #write x,y,z  [atom[0]=id, atom[1]=type]
-  print >>f,"VERTICES",len(atoms),2*len(atoms)
+  print("VERTICES", len(atoms), 2*len(atoms), file=f)
-  for i in xrange(len(atoms)):
+  for i in range(len(atoms)):
-    print >>f,1,i
+    print(1,i, file=f)
-  print >>f,"POINT_DATA",len(atoms)
+  print("POINT_DATA",len(atoms), file=f)
 
   if len(atoms) == 0:
-    print >> f
+    print('', file=f)
     f.close()
     return
 
@@ -353,9 +354,9 @@ def particleGran(file,atoms,names,n_values):
     else: # if no atoms are present
       pass
 
-    print >>f,"VECTORS",key,vectortype
+    print("VECTORS",key,vectortype, file=f)
     for atom in atoms:
-      print >>f, atom[vectors[key]], atom[vectors[key]+1], atom[vectors[key]+2]
+      print(atom[vectors[key]], atom[vectors[key]+1], atom[vectors[key]+2], file=f)
 
   # print SCALARS
   for key in scalars.keys():
@@ -368,12 +369,12 @@ def particleGran(file,atoms,names,n_values):
     else: # if no atoms are present
       pass
 
-    print >>f,"SCALARS",key,scalartype,1
+    print("SCALARS",key,scalartype,1, file=f)
-    print >>f,"LOOKUP_TABLE default"
+    print("LOOKUP_TABLE default", file=f)
     for atom in atoms:
-      print >>f, atom[scalars[key]]
+      print(atom[scalars[key]], file=f)
 
-  print >>f
+  print('', file=f)
   f.close()
 
 def findScalarsAndVectors(names):
@@ -387,7 +388,7 @@ def findScalarsAndVectors(names):
     indices[names[name]]=name
 
   # fill missing indices (occurrs e.g. if output is like vx vy vz fx fy fz vx vy vz)
-  for i in xrange(max(indices)):
+  for i in range(max(indices)):
     if i not in indices:
       indices[i]=""
 
@@ -441,7 +442,7 @@ def findScalarsAndVectors(names):
     i+=1
 
   if 'x' not in vectors.keys():
-    print "vector x y z has to be contained in dump file. please change liggghts input script accordingly."
+    print("vector x y z has to be contained in dump file. please change liggghts input script accordingly.")
     exit()
 
   return scalars, vectors

src/xyz.py

@@ -8,10 +8,14 @@
 
 # xyz tool
 
+# Imports and external programs
+
+from __future__ import print_function, absolute_import
+import sys
 oneline = "Convert LAMMPS snapshots to XYZ format"
 
 docstr = """
-x = xyz(d)		d = object containing atom coords (dump, data)
+x = xyz(d)              d = object containing atom coords (dump, data)
 
 x.one()                 write all snapshots to tmp.xyz
 x.one("new")            write all snapshots to new.xyz
@@ -29,9 +33,6 @@ x.single(N,"file")      write snapshot for timestep N to file.xyz
 # Variables
 #   data = data file to read from
 
-# Imports and external programs
-
-import sys
 
 # Class definition
 
@@ -56,18 +57,18 @@ class xyz:
       if flag == -1: break
       time,box,atoms,bonds,tris,lines = self.data.viz(which)
 
-      print >>f,len(atoms)
+      print(len(atoms), file=f)
-      print >>f,"Atoms"
+      print("Atoms", file=f)
       for atom in atoms:
         itype = int(atom[1])
-        print >>f,itype,atom[2],atom[3],atom[4]
+        print(itype,atom[2],atom[3],atom[4], file=f)
 
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       n += 1
 
     f.close()
-    print "\nwrote %d snapshots to %s in XYZ format" % (n,file)
+    print("\nwrote %d snapshots to %s in XYZ format" % (n,file))
 
   # --------------------------------------------------------------------
 
@@ -91,17 +92,17 @@ class xyz:
         file = root + str(n)
       file += ".xyz"
       f = open(file,"w")
-      print >>f,len(atoms)
+      print(len(atoms), file=f)
-      print >>f,"Atoms"
+      print("Atoms", file=f)
       for atom in atoms:
         itype = int(atom[1])
-        print >>f,itype,atom[2],atom[3],atom[4]
+        print(itype,atom[2],atom[3],atom[4], file=f)
-      print time,
+      print(time, end=' ')
       sys.stdout.flush()
       f.close()
       n += 1
 
-    print "\nwrote %s snapshots in XYZ format" % n
+    print("\nwrote %s snapshots in XYZ format" % n)
 
   # --------------------------------------------------------------------
 
@@ -113,9 +114,9 @@ class xyz:
     which = self.data.findtime(time)
     time,box,atoms,bonds,tris,lines = self.data.viz(which)
     f = open(file,"w")
-    print >>f,len(atoms)
+    print(len(atoms), file=f)
-    print >>f,"Atoms"
+    print("Atoms", file=f)
     for atom in atoms:
       itype = int(atom[1])
-      print >>f,itype,atom[2],atom[3],atom[4]
+      print(itype,atom[2],atom[3],atom[4], file=f)
     f.close()