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lammps/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py
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nbody_fix_ttree_assignments.py
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#!/usr/bin/env python
"""
nbody_fix_ttree_assignments.py
This is an ugly little script which was not intended to be run by end users.
Typical usage:
nbody_fix_ttree_assignments.py "angles" new_Angles.template \
< ttree_assignments.txt > ttree_assigmnents_new.txt
What it does:
In this example, this program extracts the first column from
"new_Angles.template", and appends to it the first column from
the lines in ttree_assignments.txt containing "@angle:".
Then it adds a second column which is just a sequence of integers
counting upwards.
Finally it inserts this 2-column text into the appropriate place in a
ttree_assignments.txt file, replacing the original @angle variables
with the new ones (followed by the renumbered original).
AWK/GREP equivalent
This program is roughly equivalent to the following lines of awk/grep:
awk 'BEGIN{i=-1} {if(substr($0,0,8)=="$/angle") i=NR; if (i==-1){print $0}}'\
< ttree_assignments.txt > ttree_assignments_new.txt
awk '{print $1}' < new_Angles.template > Angles_column1.txt
grep '$/angle:' ttree_assignments.txt | awk '{print $1}' >> Angles_column1.txt
awk '{print $1 " " NR}' < Angles_column1.txt >> ttree_assignments_new.txt
awk 'BEGIN{found=0;passed=0} {if(substr($0,0,8)=="$/angle") found=1;
else {if (found) {passed=1}}
if (passed) print $0}' \
< ttree_assignments.txt >> ttree_assignments_new.txt
I wrote this python script (instead of using awk) just to handle quoted stings
(and strings with other fancy characters and escape sequences).
"""
import sys
try:
from .ttree_lex import SplitQuotedString, InputError
except (SystemError, ValueError):
# not installed as a package
from ttree_lex import *
g_program_name = __file__.split('/')[-1]
def main():
try:
if (len(sys.argv) != 3):
raise InputError('Error running \"' + g_program_name + '\"\n'
' Wrong number of arguments.\n'
' (This is likely a programmer error.\n'
' This script was not intended to be run by end users.)\n')
cat_name = sys.argv[1]
f = open(sys.argv[2])
lines_generated = f.readlines()
f.close()
# Selections are simply lists of 2-tuples (pairs)
#f = open('ttree_assignments.txt','r')
#lines_bindings = f.readlines()
# f.close()
lines_bindings = sys.stdin.readlines()
# Figure out which lines in the 'ttree_assignments.txt' file
# contain the variables of the type you are looking for.
# Make note of the relevant line numbers
i_preexisting_begin = -1
i_preexisting_end = -1
in_section = False
possible_cat_names = set(
['$' + cat_name, '$/' + cat_name, '${' + cat_name, '${/' + cat_name])
preexisting_interaction_list = []
for i in range(0, len(lines_bindings)):
line = lines_bindings[i].strip()
tokens = SplitQuotedString(line) # strip comments, handle quotes
if len(tokens) == 2:
before_colon = tokens[0].split(':')[0]
if before_colon in possible_cat_names:
if i_preexisting_begin == -1:
i_preexisting_begin = i
in_section = True
else:
if in_section:
i_preexisting_end = i
in_section = False
if i_preexisting_end == -1:
i_preexisting_end = len(lines_bindings)
if i_preexisting_begin == -1:
for line in lines_bindings:
sys.stdout.write(line)
else:
# write out all the lines in the original file up until the point where
# the variables in the category we are looking for were encountered
for i in range(0, i_preexisting_begin):
sys.stdout.write(lines_bindings[i])
sys.stderr.write(' (adding new lines)\n')
# Now add some new lines (2-column format).
# As with any ttree_assignment.txt file:
# The first column has our generated variable names
# The second column has the counter assigned to that variable
new_counter = 1
for line_orig in lines_generated:
line = line_orig.strip()
if len(line) > 0:
tokens = SplitQuotedString(line) # strip comments, handle quotes
sys.stdout.write(tokens[0] + ' ' + str(new_counter) + '\n')
new_counter += 1
sys.stderr.write(' (adding pre-exisiting lines)\n')
if i_preexisting_begin != -1:
# Append the original pre-existing interactions of that type, but assign
# them to higher numbers. (Hopefully this helps to make sure that these
# assignments will override any of the automatic/generated assignments.)
# As with any ttree_assignment.txt file:
# The first column has our generated variable names
# The second column has the counter assigned to that variable
# sys.stderr.write(' i_preexisting_begin='+
# str(i_preexisting_begin)+
# ' i_preexisting_end='+str(i_preexisting_end)+'\n')
for i in range(i_preexisting_begin, i_preexisting_end):
line = lines_bindings[i].strip()
tokens = SplitQuotedString(line) # strip comments, handle quotes
if len(tokens) == 2:
sys.stdout.write(tokens[0] + ' ' + str(new_counter) + '\n')
new_counter += 1
#sys.stderr.write(' (writing pre-exisiting lines)\n')
# write out all the lines in the original file after this point.
for i in range(i_preexisting_end, len(lines_bindings)):
sys.stdout.write(lines_bindings[i])
sys.exit(0)
except (ValueError, InputError) as err:
sys.stderr.write('\n' + str(err) + '\n')
sys.exit(-1)
if __name__ == '__main__':
main()
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