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lammps2analisi.py
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lammps2analisi.py
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# coding=utf-8
import numpy as np
import sys
def read_write_xyz(infile,outfile,cols_pos=[3,4,5],cols_vel=None,col_id=0,col_type=1):
"""
"""
in_file = open(infile, "r")
out_file = open(outfile, "w")
#out_file.write("This Text is going to out file\nLook at it and see\n")
cont=0
while True:
if (cont%200==0):
sys.stdout.write('.')
sys.stdout.flush()
cont+=1
line=in_file.readline()
if not line: break
line=in_file.readline()
# out_file.write("ITEM: TIMESTEP\n")
# out_file.write("{}\n".format(int(round(data['step'][itimestep]))))
line=in_file.readline()
natoms=in_file.readline()
# out_file.write("ITEM: NUMBER OF ATOMS\n")
out_file.write(natoms)
line=in_file.readline()
# out_file.write('ITEM: BOX BOUNDS pp pp pp\n')
line=in_file.readline()
out_file.write(line)
line=in_file.readline()
out_file.write(line)
line=in_file.readline()
out_file.write(line)
line=in_file.readline()
# out_file.write('ITEM: ATOMS id type x y z vx vy vz\n')
for iatom in range(int(natoms)):
line = in_file.readline()
line_s=line.split()
line_o=line_s[col_id]+" "+line_s[col_type]
for col in cols_pos:
line_o += " {}".format(line_s[col])
if cols_vel != None:
for col in cols_vel:
line_o+=" {}".format(line_s[col])
else:
line_o+=" 0 0 0"
out_file.write(line_o+'\n')
out_file.close()
print "\n {} total.".format(cont)
return
if len(sys.argv)<5:
print "Uso: {} [prefix_file_in] [file_out] [col_id] [col_type] [col_pos_x col_pos_y col_pos_z] [col_vel_x col_vel_y col_vel_z] ...".format(sys.argv[0])
exit(-1)
col_pos=[3,4,5]
col_vel=None
if len(sys.argv) == 8 or len(sys.argv) == 11:
col_pos=[int(sys.argv[5]),int(sys.argv[6]),int(sys.argv[7])]
if len(sys.argv) == 11 :
col_vel=[int(sys.argv[8]),int(sys.argv[9]),int(sys.argv[10])]
print "velocities: ", col_vel
print "positions: ", col_pos
print "id: ", int(sys.argv[3])
print "type: ",int(sys.argv[4])
read_write_xyz(sys.argv[1],sys.argv[2],col_pos,col_vel,int(sys.argv[3]),int(sys.argv[4]))