mEff_err = np.std(mEff, axis=0) * float(binNum - 1) / math.sqrt(float(binNum))
######################
# Write output files #
######################
# Two-point functions
outputFilename = output_template.replace("*", "twop")
avgOutputFilename = output_template.replace("*", "twop_avg")
rw.writeDataFile(twop_jk, outputFilename)
rw.writeAvgDataFile(twop_avg, twop_err, avgOutputFilename)
print "Wrote two-point function files"
# Effective mass
outputFilename = output_template.replace("*", "mEff")
avgOutputFilename = output_template.replace("*", "mEff_avg")
rw.writeDataFile(mEff, outputFilename)
rw.writeAvgDataFile(mEff_avg, mEff_err, avgOutputFilename)
print "Wrote effective mass files"
threep = threep_gtDt - 0.25 * ( threep_gtDt + threep_gxDx + threep_gyDy + threep_gzDz )
# Jackknife
# threep_jk[ ts ][ b, t ]
threep_jk.append( fncs.jackknife( threep, binSize ) )
threep_jk_cp = fncs.jackknife( threep, binSize )
threep_avg = np.average( threep_jk_cp, axis=0 )
threep_err = np.std( threep_jk_cp, axis=0 ) * float( binNum - 1 ) / np.sqrt( float( binNum ) )
avgOutputFilename = output_template.replace( "*", "threep_tsink" + str( ts ) )
rw.writeAvgDataFile( threep_avg, threep_err, avgOutputFilename )
# End loop over tsink
avgOutputFilename = output_template.replace( "*", "twop_avg" )
rw.writeAvgDataFile( twop_avg, twop_err, avgOutputFilename )
##################
# Two-state Fit #
##################
fit = fncs.twoStateFit( twop_ts, threep_jk )
# Average over bins
######
# gA #
######
# Calculate
# gA[ b, t ]
gA = Z * pq.calcgA(threep_jk, twop_jk[:, ts])
print "gA:"
print gA
# Average over bins
# gA_avg[ t ]
gA_avg = np.average(gA, axis=0)
gA_err = np.std(gA, axis=0) * float(binNum - 1) / np.sqrt(float(binNum))
# Write output files
gA_outFilename = output_template.replace("*", "gA_tsink" + str(ts))
rw.writeAvgDataFile(gA_avg, gA_err, gA_outFilename)
print "Wrote output files for tsink " + str(ts)
# End loop over tsink
# Average over bins
avgX_avg = np.average( avgX, axis=0 )
avgX_err = np.std( avgX, axis=0 ) * float( binNum - 1 ) / np.sqrt( float( binNum ) )
######################
# Write output files #
######################
# <x>
avgX_outFilename = output_template.replace( "*", "avgX_tsink" + str( ts ) )
rw.writeAvgDataFile( avgX_avg, avgX_err, avgX_outFilename )
# Fitted effective mass
mEff_outputFilename = output_template.replace( "*", "mEff_fit" )
rw.writeFitDatafile( mEff_outputFilename, mEff_fit_avg, mEff_fit_err, mEff_fitStart, mEff_fitEnd )
###############
# Fit plateau #
###############
fitStart = []
fitEnd = []