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correlate.py
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Mon, Nov 4, 09:40

correlate.py
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#!/usr/bin/python
"""
function:
parse the block of thermo data in a lammps logfile and perform auto- and
cross correlation of the specified column data. The total sum of the
correlation is also computed which can be converted to an integral by
multiplying by the timestep.
output:
standard output contains column data for the auto- & cross correlations
plus the total sum of each. Note, only the upper triangle of the
correlation matrix is computed.
usage:
correlate.py [-c col] <-c col2> <-s max_correlation_time> [logfile]
"""
import sys
import re
import array
# parse command line
maxCorrelationTime = 0
cols = array.array("I")
nCols = 0
args = sys.argv[1:]
index = 0
while index < len(args):
arg = args[index]
index += 1
if (arg == "-c"):
cols.append(int(args[index])-1)
nCols += 1
index += 1
elif (arg == "-s"):
maxCorrelationTime = int(args[index])
index += 1
else :
filename = arg
if (nCols < 1): raise RuntimeError, 'no data columns requested'
data = [array.array("d")]
for s in range(1,nCols) : data.append( array.array("d") )
# read data block from log file
start = False
input = open(filename)
nSamples = 0
pattern = re.compile('\d')
line = input.readline()
while line :
columns = line.split()
if (columns and pattern.match(columns[0])) :
for i in range(nCols):
data[i].append( float(columns[cols[i]]) )
nSamples += 1
start = True
else :
if (start) : break
line = input.readline()
print "# read :",nSamples," samples of ", nCols," data"
if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
# correlate and integrate
correlationPairs = []
for i in range(0,nCols):
for j in range(i,nCols): # note only upper triangle of the correlation matrix
correlationPairs.append([i,j])
header = "# "
for k in range(len(correlationPairs)):
i = str(correlationPairs[k][0]+1)
j = str(correlationPairs[k][1]+1)
header += " C"+i+j+" sum_C"+i+j
print header
nCorrelationPairs = len(correlationPairs)
sum = [0.0] * nCorrelationPairs
for s in range(maxCorrelationTime) :
correlation = [0.0] * nCorrelationPairs
nt = nSamples-s
for t in range(0,nt) :
for p in range(nCorrelationPairs):
i = correlationPairs[p][0]
j = correlationPairs[p][1]
correlation[p] += data[i][t]*data[j][s+t]
output = ""
for p in range(0,nCorrelationPairs):
correlation[p] /= nt
sum[p] += correlation[p]
output += str(correlation[p]) + " " + str(sum[p]) + " "
print output

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