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