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lammps/tools/moltemplate/src/raw2data.py
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raw2data.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from dump2data import *
g_program_name = 'raw2data.py'
g_date_str = '2014-12-19'
g_version_str = 'v0.43'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str)
sys.stderr.write('\n')
try:
data_settings = DataSettings()
misc_settings = MiscSettings()
misc_settings.multi = False
warning_strings = []
ParseArgs(sys.argv,
misc_settings,
data_settings,
warning_strings)
frame_coords = defaultdict(list)
frame_coords_ixiyiz = defaultdict(list)
frame_vects = defaultdict(list)
frame_velocities = defaultdict(list)
frame_xlo_str = frame_xhi_str = None
frame_ylo_str = frame_yhi_str = None
frame_zlo_str = frame_zhi_str = None
frame_xy_str = frame_xz_str = frame_yz_str = None
frame_natoms = -1
frame_timestep_str = ''
i_atomid = i_atomtype = i_molid = -1
i_x = i_y = i_z = i_xu = i_yu = i_zu = -1
i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1
dump_column_names = []
#num_frames_in = -1
num_frames_out = 0
finished_reading_frame = False
read_last_frame = False
#in_coord_file = open('traj.raw','r')
#in_coord_file = open('tmp_atom_coords.dat','r')
in_coord_file = sys.stdin
read_last_frame = False
while True:
line = '\n'
while (line != '') and (line.strip() == ''):
line = in_coord_file.readline()
if line == '': # if EOF
break
frame_coords = defaultdict(list)
while line.strip() != '':
n_crds = len(frame_coords)
#sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n")
frame_coords[str(n_crds+1)] = line.split()
line = in_coord_file.readline()
# Check to see if there are any blank lines at this location in the file
# If there are, it means we are at a new "frame" (in the trajectory).
# Skip over any blank line(s) separating this frame from the next frame
# so that the next time we enter the loop, we are at the beginning
# of a new frame.
while (line != '') and (line.strip() == ''):
line = in_coord_file.readline()
# Parse the DATA file specified by the user
# and replace appropriate lines or fields with
# the corresponding text from the input file.
if misc_settings.multi:
out_file_name = data_settings.file_name + '.'\
+ str(num_frames_out)
sys.stderr.write(' (creating file \"'+out_file_name+'\")\n')
out_file = open(out_file_name, 'w')
else:
out_file = sys.stdout
WriteFrameToData(out_file,
None,
misc_settings,
data_settings,
frame_natoms,
frame_coords,
frame_coords_ixiyiz,
frame_vects,
frame_velocities,
None,
None,
frame_xlo_str, frame_xhi_str,
frame_ylo_str, frame_yhi_str,
frame_zlo_str, frame_zhi_str,
frame_xy_str, frame_xz_str, frame_yz_str)
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)
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