get rid of (evil) tabs and trailing whitespace in bundled Pizza.py components

tools/python/pizza/cfg.py

@@ -11,7 +11,7 @@
 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

tools/python/pizza/dump.py

@@ -12,15 +12,15 @@ 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
   atoms will be unscaled if stored in files as scaled
   self-describing column names assigned
 
-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 +32,20 @@ d.map(1,"id",3,"x")               assign names to 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 +56,24 @@ 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
     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 +85,8 @@ 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
@@ -107,17 +107,17 @@ 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
 
   atom() returns vectors with one value for each selected timestep
   vecs() returns vectors with one value for each selected atom in the timestep
 
-index,time,flag = d.iterator(0/1)          loop over dump snapshots
+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.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
@@ -304,15 +304,15 @@ 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

tools/python/pizza/gnu.py

@@ -11,12 +11,12 @@
 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 +29,21 @@ 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:
 

tools/python/pizza/log.py

@@ -28,7 +28,7 @@ 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
@@ -133,9 +133,9 @@ class log:
       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:
@@ -161,9 +161,9 @@ class log:
         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:
@@ -226,7 +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
 
@@ -236,7 +236,7 @@ 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)
@@ -275,36 +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

tools/python/pizza/xyz.py

@@ -11,7 +11,7 @@
 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