Cleanup trailing spaces in util scripts

util/get_atomset.sh

@@ -4,5 +4,5 @@
 # use: get_atomset sample.xml
 #
 nlines=$(grep /atomset -m 1 -n $1 | cut -f1 -d: - )
-head -$nlines $1 
+head -$nlines $1
 echo "</fpmd:sample>"

util/qbox_dos.py

@@ -36,7 +36,7 @@ de = (emax - emin)/(ndos-1)
 # f(x) = 1/(sqrt(pi)*width) * exp(-(x/width)^2 )
 def gauss(x, width):
   return (1.0/(math.sqrt(math.pi)*width)) * math.exp(-(x/width)**2)
-  
+
 # Qbox output handler to extract and process data
 class QboxOutputHandler(xml.sax.handler.ContentHandler):
   def __init__(self):

util/qbox_repair_h2o.py

@@ -73,9 +73,9 @@ for h in hlist:
     print "# current ",h[1]," at ", h[3],h[4],h[5]
     print "# nearest O is at ", nearest_o[3],nearest_o[4],nearest_o[5]
     print "# move ",h[1]," by ", sx_min, sy_min, sz_min
-    h[3] += sx_min    
-    h[4] += sy_min    
-    h[5] += sz_min    
+    h[3] += sx_min
+    h[4] += sy_min
+    h[5] += sz_min
 
 for o in olist:
   print o[0],o[1],o[2],'%10.5f'%o[3],'%10.5f'%o[4],'%10.5f'%o[5]

util/qbox_species_temp.sh

@@ -7,7 +7,7 @@
 # use: qbox_species_temp.sh species_name file [file ...]
 #
 if (($#<2))
- then echo " use: qbox_species_temp.sh species file [file ...]" 
+ then echo " use: qbox_species_temp.sh species file [file ...]"
       exit 1
 fi
 species=$1

util/qbox_translate.sh

 #!/bin/bash
-# qbox_translate: translate all atoms 
+# qbox_translate: translate all atoms
 # use: qbox_replicate cell.sys dx dy dz > newcell.sys
 #
 if (( $# != 4 ))

util/qbox_xyz.py

@@ -3,7 +3,7 @@
 # This file is part of Qbox
 #
 # qbox_xyz.py: extract sets of atomic positions in xyz format
-# from a Qbox output file or from a Qbox sample file using SAX 
+# from a Qbox output file or from a Qbox sample file using SAX
 # incremental parsing
 #
 # use: qbox_xyz.py [-first] {file|URL}

util/qso.py

@@ -45,10 +45,10 @@ class AtomSet:
 class Sample:
   def __init__(self):
     self.atoms = AtomSet()
- 
+
 # The following handler processes the <atomset> element of
 # an XML document and updates the AtomSet data of the Sample
-# If multiple instances of <atomset> are found, the 
+# If multiple instances of <atomset> are found, the
 # handler overwrites the AtomSet data
 class QSOAtomSetHandler(xml.sax.handler.ContentHandler):
   def __init__(self,sample):
@@ -73,7 +73,7 @@ class QSOAtomSetHandler(xml.sax.handler.ContentHandler):
       self.s.atoms.cell.a = attributes["a"]
       self.s.atoms.cell.b = attributes["b"]
       self.s.atoms.cell.c = attributes["c"]
-    elif (name == "species"): 
+    elif (name == "species"):
       self.inSpecies = True
       self.species_name = "species_name"
       if "name" in attributes:
@@ -83,9 +83,9 @@ class QSOAtomSetHandler(xml.sax.handler.ContentHandler):
         self.species_href = attributes["href"]
       self.species_symbol = self.species_name+"_symbol"
       self.species_atomic_number = self.species_name+"_atomic_number"
-      self.species_mass = self.species_name+"_mass" 
+      self.species_mass = self.species_name+"_mass"
     elif (name == "atom") and self.inAtomSet:
-      self.inAtom = True 
+      self.inAtom = True
       self.atom_name = attributes["name"]
       self.atom_species = attributes["species"]
       sp = Species(self.species_name,self.species_href,self.species_symbol,
@@ -124,7 +124,7 @@ class QSOAtomSetHandler(xml.sax.handler.ContentHandler):
       x = float(pos[0])
       y = float(pos[1])
       z = float(pos[2])
-      self.atom_position = [x,y,z] 
+      self.atom_position = [x,y,z]
       self.inPosition = False
     if (name == "velocity") and self.inAtom:
       vel = self.buffer.split()

util/qso2qbox.py

 #!/usr/bin/python
-# Convert <atomset> elements from quantum-simulation.org (QSO) format 
+# Convert <atomset> elements from quantum-simulation.org (QSO) format
 # to Qbox input file
 # use: qso2qbox.py [-last] {file|URL}
 # Default: only the first <atomset> element is processed
@@ -10,7 +10,7 @@ import os.path
 import xml.sax
 import sys
 import urllib2
-import datetime 
+import datetime
 
 def usage():
   print "use: ",sys.argv[0]," [-last] {file|URL}"

util/sample_to_move.sh

@@ -18,7 +18,7 @@ xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">
 </xsl:template>
 <xsl:template match="atom">
   <xsl:text>move </xsl:text>
-  <xsl:value-of select="@name"/> 
+  <xsl:value-of select="@name"/>
   <xsl:text> to </xsl:text>
   <xsl:value-of select="position"/> <xsl:text>
 </xsl:text>

util/sample_to_sys.sh

@@ -32,8 +32,8 @@ xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">
   <xsl:text>atom </xsl:text>
   <xsl:value-of select="@name"/> <xsl:text> </xsl:text>
   <xsl:value-of select="@species"/> <xsl:text> </xsl:text>
-  <xsl:value-of select="position"/>  <xsl:text> </xsl:text> 
-  <xsl:value-of select="velocity"/> <xsl:text> 
+  <xsl:value-of select="position"/>  <xsl:text> </xsl:text>
+  <xsl:value-of select="velocity"/> <xsl:text>
 </xsl:text>
 </xsl:template>
 <xsl:template match="*"/>