#!@PYTHON@
#
# Removes random atoms from a TREMOLO data file

import sys, random

# check arguments
if len(sys.argv) < 2:
  print "Usage: "+sys.argv[0]+" <datafile> <NoDefects>"
  sys.exit(1)

input = open(sys.argv[1], "r")
output = open(sys.argv[1]+".defect", "w")
defectcount=int(sys.argv[2])

# parse lines into array
lines=[]
comments=0
nr=0
for line in input:
  if "#" in line:
    comments=comments+1
  lines.append(line)
nr=len(lines)
input.close()
print "I have scanned "+str(nr)+" lines in "+sys.argv[1]+" with "+str(comments)+" comments."

if (nr-comments)>int(defectcount):
  for i in range(defectcount):
    while True:
      linenr=random.randint(comments,nr-1)
      if not "removed" in lines[linenr]:
        lines[linenr]="removed"
        break
else:
  print "There are fewer atoms present than you want removed, aborting." 
  sys.exit(1)
print "I have removed "+str(defectcount)+" atoms."

for i in range(nr):
  if not "removed" in lines[i]:
    output.write(lines[i])
output.close()
print "I have stored the new configuration."

print "All done."

sys.exit(0)