git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4859 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/eff/lmp2data.py

@@ -0,0 +1,144 @@
+#!/usr/local/bin/python-2.5/bin/python
+
+Info="""
+Module name: lmp2data.py 
+
+Author: (c) Andres Jaramillo-Botero
+California Institute of Technology
+ajaramil@wag.caltech.edu
+Project: pEFF
+Version: August 2009
+
+Extracts the electron radii from a lammps trajectory dump of style custom:
+
+dump    1 all custom period dump_file id type x y z spin radius ...
+
+NOTE: The radius must be the i'th column per trajectory entry in the dump file
+
+"""
+
+# import essentials: 
+import sys, os 
+from math import log10
+from shutil import rmtree 
+from getopt import gnu_getopt as getopt
+import numpy
+
+def printHelp():
+    print Info
+    print "Usage: python lmp2data.py test.lammpstrj\n"
+    return
+
+def makeradii(infile,outfile,column,flag_all):
+
+    print "Reading %s ... [WAIT]"%infile,
+    fin = open(infile,'r')
+    lines = fin.xreadlines()
+    print 7*"\b"+"[DONE]"
+    frame=0
+    radii=[]
+    # grep the number of frames and atoms/frame
+    os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms; grep -m 1 \"ITEM: ATOMS\" %s > params"%(infile,infile,infile))
+    tmp=open("frames",'r')
+    frames=int(tmp.readline().split()[0])
+    tmp.close()
+    tmp=open("atoms",'r')
+    atoms=int(tmp.readlines()[1].split()[0])
+    tmp.close()
+    tmp=open("params",'r')
+    ids=tmp.readline().split()[2:]
+    os.system("rm -rf frames atoms params")
+    arry=numpy.zeros((atoms,frames),dtype=str)
+    framecnt=0
+    header=9
+    ecount=0
+    if flag_all==True: atom_type="nuclei and electron"
+    else: atom_type="electron"
+    print "Extracting %s %s per frame from %s ...  "%(atom_type,ids[column],infile),
+    for i,line in enumerate(lines):
+      lo=(atoms+header)*framecnt+header
+      hi=lo+atoms
+      if (i<lo): 
+        continue
+      elif (i >= lo) and (i < hi):
+        lparse=line.split()
+        id=int(lparse[0])
+#        r=float(lparse[column-1])
+        r=lparse[column]
+#        if (float(r)!=0):
+        arry[id-1][framecnt]=r
+        print arry[id-1][framecnt],r,raw_input()
+        if (float(r)!=0) and (framecnt==0): ecount+=1
+#        else: arry[id-1][framecnt]=r
+        if (i==lo+1): 
+          sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b"))
+          sys.stdout.flush()
+      if (i == hi+1): 
+        framecnt+=1
+
+    print
+    if outfile=="": 
+      outfile=infile+'.%s'%(ids[column])
+      fout=open(outfile,'w')
+    else: fout=open(outfile,'w')
+    print "Writing %s/frame table to %s ... "%(ids[column],outfile),
+    sys.stdout.flush()
+
+    for i in range(frames):
+      fout.writelines('\tF'+str(i))
+    fout.writelines("\n")
+    e=1
+    for a in range(atoms):
+      if flag_all==True:
+        sys.stdout.write("%d/%d%s"%(a+1,atoms,(int(log10(a+1))+int(log10(atoms))+3)*"\b"))
+        sys.stdout.flush()
+        fout.writelines("%d\t"%(a+1))
+        for f in range(frames):
+          fout.writelines("%s\t"%(arry[a][f]))
+        fout.writelines("\n")
+      else:
+        if arry[a][0] == 0.0:
+          continue
+        else:
+          sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b"))
+          sys.stdout.flush()
+          e+=1
+          fout.writelines("%d\t"%(a+1))
+          for f in range(frames):
+            fout.writelines("%s\t"%(arry[a][f]))
+          fout.writelines("\n")
+
+    print
+    print "DONE .... GOODBYE !!"
+    fout.close()
+    fin.close()
+
+if __name__ == '__main__':
+
+    # set defaults
+    outfile = ""
+    flag_all = False
+    column=6	# default = radius
+
+    # check for input:
+    opts, argv = getopt(sys.argv[1:], 'c:o:ha')
+
+    # if no input, print help and exit
+    if len(argv) != 1:
+        printHelp()
+        sys.exit(1)
+    else:
+        infile=argv[0]
+
+    # read options
+    for opt, arg in opts:
+        if opt == '-h':             # -h: print help
+          printHelp()
+        if opt == '-o':		# output file name
+          outfile=arg
+        if opt == '-a':		# all nuclii+electrons
+          flag_all=True
+        if opt == '-c':		# select column from lammpstrj file to tabulate
+          column=int(arg)
+
+    makeradii(infile,outfile,column,flag_all)