[ViewVC] Annotation of: OpenMD/branches/heatflux/src/applications/utilities/stat2thcond

#!/usr/bin/env python
"""Heat Flux Correlation function

Computes the correlation function of the heat flux vector
that has been stored in a stat file.   These can be used to compute
the thermal conductivity.

Usage: stat2thcond

Options:
  -h, --help              show this help
  -f, --stat-file=...     use specified stat file
  -o, --output-file=...   use specified output (.pcorr) file
  -e, --einstein          use Einstein relation (based on Hess 2002 paper)

The Einstein relation option will compute: V*<(\int_0^t (S(t')-<S>)dt')^2>/2kT^2,
which will grow approximately linearly in time.  The long-time slope of this
function will be the viscosity.

Example:
   stat2thcond -f ring5.stat -o ring5.pcorr

"""

__author__ = "Dan Gezelter (gezelter@nd.edu)"
__version__ = "$Revision: 1665 $"
__date__ = "$Date: 2011-12-08 15:25:26 -0400 (Thu, 9 December 2011) $"

__copyright__ = "Copyright (c) 2007 by the University of Notre Dame"
__license__ = "OpenMD"

import sys
import getopt
import string
import math

def usage():
    print __doc__

def readStatFile(statFileName):

    global time
    global temperature
    global pressure
    global volume
    global Sx
    global Sy
    global Sz
    time = []
    temperature = []
    pressure = []
    volume = []
    Sx = []
    Sy = []
    Sz = []

    statFile = open(statFileName, 'r')
    line = statFile.readline()

    print "reading File"
    pressSum = 0.0
    volSum = 0.0
    tempSum = 0.0
    line = statFile.readline()
    while 1:
        L = line.split()
        time.append(float(L[0]))
        temperature.append(float(L[4]))
        #
        # OpenMD prints out pressure in units of atm.
        #
        pressure.append(float(L[5]))
        volume.append(float(L[6]))
        #
        # OpenMD prints out heatflux in units of kcal / (mol s Ang^2).
        #
        Sx.append(float(L[8]))
        Sy.append(float(L[9]))
        Sz.append(float(L[10]))

        line = statFile.readline()
        if not line: break

    statFile.close()

def computeAverages():

    global tempAve
    global pressAve
    global volAve
    global pvAve

    print "computing Averages"

    tempSum = 0.0
    pressSum = 0.0
    volSum = 0.0
    pvSum = 0.0

    temp2Sum = 0.0
    press2Sum = 0.0
    vol2Sum = 0.0
    pv2Sum = 0.0

    # converts amu*fs^-2*Ang^-1 -> atm
    pressureConvert = 1.63882576e8

    for i in range(len(time)):
        tempSum = tempSum + temperature[i]
        pressSum = pressSum + pressure[i]
        volSum = volSum + volume[i]
        # in units of amu Ang^2 fs^-1
        pvTerm = pressure[i]*volume[i] / pressureConvert
        pvSum = pvSum + pvTerm
        temp2Sum = temp2Sum + math.pow(temperature[i],2)
        press2Sum = press2Sum + math.pow(pressure[i],2)
        vol2Sum = vol2Sum + math.pow(volume[i],2)
        pv2Sum = pv2Sum + math.pow(pvTerm,2)

    tempAve = tempSum / float(len(time))
    pressAve = pressSum / float(len(time))
    volAve = volSum / float(len(time))
    pvAve = pvSum / float(len(time))

    tempSdev = math.sqrt(temp2Sum / float(len(time)) - math.pow(tempAve,2))
    pressSdev = math.sqrt(press2Sum / float(len(time)) - math.pow(pressAve,2))
    if (vol2Sum / float(len(time)) < math.pow(volAve,2)):
        volSdev = 0.0
    else:
        volSdev = math.sqrt(vol2Sum / float(len(time)) - math.pow(volAve,2))
    pvSdev = math.sqrt(pv2Sum / float(len(time)) - math.pow(pvAve,2))

    print "   Average pressure = %f +/- %f (atm)" % (pressAve, pressSdev)
    print "     Average volume = %f +/- %f (Angst^3)" % (volAve, volSdev)
    print "Average temperature = %f +/- %f (K)" % (tempAve, tempSdev)
    print " Average PV product = %f +/- %f (amu Angst^2 fs^-1)" % (pvAve, pvSdev)

def computeCorrelations(outputFileName):

    # converts amu*fs^-2*Ang^-1 -> atm
    pressureConvert = 1.63882576e8

    # converts Ang^-3 * kcal/mol * Ang / fs to m^-3 * J/mol * m /s (= W / mol m^2)
    heatfluxConvert = 4.187e38

    # converts fs to s
    dtConvert = 1e-15

    # Boltzmann's constant amu*Ang^2*fs^-2/K
    # kB = 8.31451e-7

    # Boltzmann's constant kcal/K
    kB = 3.29762e-27

    # converts (amu/fs^3)^2*fs^2 --> kcal^2/angstrom^4
    intSSdtdtConvert = 1.57288e-41


    # preV = thcondConvert * volAve / (kB * tempAve * tempAve)

    # Without unit conversions as follows it should be in Ang^3 / (kcal K)
    preV = volAve / (kB * tempAve * tempAve)

    if doEinstein:
        print "computing Einstein-style Correlation Function"

        # Precompute sum variables to aid integration.
        # The integral from t0 -> t0 + t  can be easily obtained
        # from the precomputed sum variables:  sum[t0+t] - sum[t0-1]
        #for i in range(1, len(time)):
        xSum = []       
        xSum.append(Sx[0])
        ySum = []
        ySum.append(Sy[0])
        zSum = []
        zSum.append(Sz[0])
        for i in range(1, len(time)):
            xSum.append(xSum[i-1] + Sx[i])
            ySum.append(ySum[i-1] + Sy[i])
            zSum.append(zSum[i-1] + Sz[i])

        dt = time[1] - time[0]

        eXcorr = []
        eYcorr = []
        eZcorr = []

        # i corresponds to the total duration of the integral
        for i in range(len(time)):

            xIntSum = 0.0
            yIntSum = 0.0
            zIntSum = 0.0
            # j corresponds to the starting point of the integral
            for j in range(len(time) - i):
                if (j == 0):

                    xInt = dt*xSum[j+i]
                    yInt = dt*ySum[j+i]
                    zInt = dt*zSum[j+i]
                else:
                    xInt = dt*(xSum[j+i] - xSum[j-1])
                    yInt = dt*(ySum[j+i] - ySum[j-1])
                    zInt = dt*(zSum[j+i] - zSum[j-1])

                xIntSum = xIntSum + xInt*xInt
                yIntSum = yIntSum + yInt*yInt
                zIntSum = zIntSum + zInt*zInt

            eXcorr.append(xIntSum / float(len(time)-i))
            eYcorr.append(yIntSum / float(len(time)-i))
            eZcorr.append(zIntSum / float(len(time)-i))


    outputFile = open(outputFileName, 'w')
    for i in range(len(time)):

        if doEinstein:
            # outputFile.write("%f\t%13e\n" % (time[i], 0.5 * preV * heatfluxConvert * heatfluxConvert * dtConvert * dtConvert * (eXcorr[i] + eYcorr[i] + eZcorr[i])))
            outputFile.write("%f\t%13e\n" % (time[i], 0.5 * preV * intSSdtdtConvert * (eXcorr[i] + eYcorr[i] + eZcorr[i])))
                                              # Ang^3 / (kcal K)   *       kcal^2/angstrom^4
    outputFile.close()

def main(argv):
    global doEinstein
    global haveStatFileName
    global haveOutputFileName

    haveStatFileName = False
    haveOutputFileName = False
    doEinstein = False

    try:
        opts, args = getopt.getopt(argv, "hgesf:o:", ["help", "einstein", "stat-file=", "output-file="])
    except getopt.GetoptError:
        usage()
        sys.exit(2)
    for opt, arg in opts:
        if opt in ("-h", "--help"):
            usage()
            sys.exit()
        elif opt in ("-e", "--einstein"):
            doEinstein = True
        elif opt in ("-f", "--stat-file"):
            statFileName = arg
            haveStatFileName = True
        elif opt in ("-o", "--output-file"):
            outputFileName = arg
            haveOutputFileName = True
    if (not haveStatFileName):
        usage()
        print "No stat file was specified"
        sys.exit()
    if (not haveOutputFileName):
        usage()
        print "No output file was specified"
        sys.exit()

    readStatFile(statFileName);
    computeAverages();
    computeCorrelations(outputFileName);

if __name__ == "__main__":
    if len(sys.argv) == 1:
        usage()
        sys.exit()
    main(sys.argv[1:])
Revision:	1675
Committed:	Thu Feb 16 17:17:24 2012 UTC (13 years, 6 months ago) by chuckv
File size:	7889 byte(s)
Log Message:	Updated version of Gianluca's stat2thcond.
#	User	Rev	Content
1	chuckv	1675	#!/usr/bin/env python
2			"""Heat Flux Correlation function
3
4			Computes the correlation function of the heat flux vector
5			that has been stored in a stat file. These can be used to compute
6			the thermal conductivity.
7
8			Usage: stat2thcond
9
10			Options:
11			-h, --help show this help
12			-f, --stat-file=... use specified stat file
13			-o, --output-file=... use specified output (.pcorr) file
14			-e, --einstein use Einstein relation (based on Hess 2002 paper)
15
16			The Einstein relation option will compute: V*<(\int_0^t (S(t')-<S>)dt')^2>/2kT^2,
17			which will grow approximately linearly in time. The long-time slope of this
18			function will be the viscosity.
19
20			Example:
21			stat2thcond -f ring5.stat -o ring5.pcorr
22
23			"""
24
25			__author__ = "Dan Gezelter (gezelter@nd.edu)"
26			__version__ = "$Revision: 1665 $"
27			__date__ = "$Date: 2011-12-08 15:25:26 -0400 (Thu, 9 December 2011) $"
28
29			__copyright__ = "Copyright (c) 2007 by the University of Notre Dame"
30			__license__ = "OpenMD"
31
32			import sys
33			import getopt
34			import string
35			import math
36
37			def usage():
38			print __doc__
39
40			def readStatFile(statFileName):
41
42			global time
43			global temperature
44			global pressure
45			global volume
46			global Sx
47			global Sy
48			global Sz
49			time = []
50			temperature = []
51			pressure = []
52			volume = []
53			Sx = []
54			Sy = []
55			Sz = []
56
57			statFile = open(statFileName, 'r')
58			line = statFile.readline()
59
60			print "reading File"
61			pressSum = 0.0
62			volSum = 0.0
63			tempSum = 0.0
64			line = statFile.readline()
65			while 1:
66			L = line.split()
67			time.append(float(L[0]))
68			temperature.append(float(L[4]))
69			#
70			# OpenMD prints out pressure in units of atm.
71			#
72			pressure.append(float(L[5]))
73			volume.append(float(L[6]))
74			#
75			# OpenMD prints out heatflux in units of kcal / (mol s Ang^2).
76			#
77			Sx.append(float(L[8]))
78			Sy.append(float(L[9]))
79			Sz.append(float(L[10]))
80
81			line = statFile.readline()
82			if not line: break
83
84			statFile.close()
85
86			def computeAverages():
87
88			global tempAve
89			global pressAve
90			global volAve
91			global pvAve
92
93			print "computing Averages"
94
95			tempSum = 0.0
96			pressSum = 0.0
97			volSum = 0.0
98			pvSum = 0.0
99
100			temp2Sum = 0.0
101			press2Sum = 0.0
102			vol2Sum = 0.0
103			pv2Sum = 0.0
104
105			# converts amufs^-2Ang^-1 -> atm
106			pressureConvert = 1.63882576e8
107
108			for i in range(len(time)):
109			tempSum = tempSum + temperature[i]
110			pressSum = pressSum + pressure[i]
111			volSum = volSum + volume[i]
112			# in units of amu Ang^2 fs^-1
113			pvTerm = pressure[i]*volume[i] / pressureConvert
114			pvSum = pvSum + pvTerm
115			temp2Sum = temp2Sum + math.pow(temperature[i],2)
116			press2Sum = press2Sum + math.pow(pressure[i],2)
117			vol2Sum = vol2Sum + math.pow(volume[i],2)
118			pv2Sum = pv2Sum + math.pow(pvTerm,2)
119
120			tempAve = tempSum / float(len(time))
121			pressAve = pressSum / float(len(time))
122			volAve = volSum / float(len(time))
123			pvAve = pvSum / float(len(time))
124
125			tempSdev = math.sqrt(temp2Sum / float(len(time)) - math.pow(tempAve,2))
126			pressSdev = math.sqrt(press2Sum / float(len(time)) - math.pow(pressAve,2))
127			if (vol2Sum / float(len(time)) < math.pow(volAve,2)):
128			volSdev = 0.0
129			else:
130			volSdev = math.sqrt(vol2Sum / float(len(time)) - math.pow(volAve,2))
131			pvSdev = math.sqrt(pv2Sum / float(len(time)) - math.pow(pvAve,2))
132
133			print " Average pressure = %f +/- %f (atm)" % (pressAve, pressSdev)
134			print " Average volume = %f +/- %f (Angst^3)" % (volAve, volSdev)
135			print "Average temperature = %f +/- %f (K)" % (tempAve, tempSdev)
136			print " Average PV product = %f +/- %f (amu Angst^2 fs^-1)" % (pvAve, pvSdev)
137
138			def computeCorrelations(outputFileName):
139
140			# converts amufs^-2Ang^-1 -> atm
141			pressureConvert = 1.63882576e8
142
143			# converts Ang^-3 * kcal/mol * Ang / fs to m^-3 * J/mol * m /s (= W / mol m^2)
144			heatfluxConvert = 4.187e38
145
146			# converts fs to s
147			dtConvert = 1e-15
148
149			# Boltzmann's constant amuAng^2fs^-2/K
150			# kB = 8.31451e-7
151
152			# Boltzmann's constant kcal/K
153			kB = 3.29762e-27
154
155			# converts (amu/fs^3)^2*fs^2 --> kcal^2/angstrom^4
156			intSSdtdtConvert = 1.57288e-41
157
158
159			# preV = thcondConvert * volAve / (kB * tempAve * tempAve)
160
161			# Without unit conversions as follows it should be in Ang^3 / (kcal K)
162			preV = volAve / (kB * tempAve * tempAve)
163
164			if doEinstein:
165			print "computing Einstein-style Correlation Function"
166
167			# Precompute sum variables to aid integration.
168			# The integral from t0 -> t0 + t can be easily obtained
169			# from the precomputed sum variables: sum[t0+t] - sum[t0-1]
170			#for i in range(1, len(time)):
171			xSum = []
172			xSum.append(Sx[0])
173			ySum = []
174			ySum.append(Sy[0])
175			zSum = []
176			zSum.append(Sz[0])
177			for i in range(1, len(time)):
178			xSum.append(xSum[i-1] + Sx[i])
179			ySum.append(ySum[i-1] + Sy[i])
180			zSum.append(zSum[i-1] + Sz[i])
181
182			dt = time[1] - time[0]
183
184			eXcorr = []
185			eYcorr = []
186			eZcorr = []
187
188			# i corresponds to the total duration of the integral
189			for i in range(len(time)):
190
191			xIntSum = 0.0
192			yIntSum = 0.0
193			zIntSum = 0.0
194			# j corresponds to the starting point of the integral
195			for j in range(len(time) - i):
196			if (j == 0):
197
198			xInt = dt*xSum[j+i]
199			yInt = dt*ySum[j+i]
200			zInt = dt*zSum[j+i]
201			else:
202			xInt = dt*(xSum[j+i] - xSum[j-1])
203			yInt = dt*(ySum[j+i] - ySum[j-1])
204			zInt = dt*(zSum[j+i] - zSum[j-1])
205
206			xIntSum = xIntSum + xInt*xInt
207			yIntSum = yIntSum + yInt*yInt
208			zIntSum = zIntSum + zInt*zInt
209
210			eXcorr.append(xIntSum / float(len(time)-i))
211			eYcorr.append(yIntSum / float(len(time)-i))
212			eZcorr.append(zIntSum / float(len(time)-i))
213
214
215			outputFile = open(outputFileName, 'w')
216			for i in range(len(time)):
217
218			if doEinstein:
219			# outputFile.write("%f\t%13e\n" % (time[i], 0.5 * preV * heatfluxConvert * heatfluxConvert * dtConvert * dtConvert * (eXcorr[i] + eYcorr[i] + eZcorr[i])))
220			outputFile.write("%f\t%13e\n" % (time[i], 0.5 * preV * intSSdtdtConvert * (eXcorr[i] + eYcorr[i] + eZcorr[i])))
221			# Ang^3 / (kcal K) * kcal^2/angstrom^4
222			outputFile.close()
223
224			def main(argv):
225			global doEinstein
226			global haveStatFileName
227			global haveOutputFileName
228
229			haveStatFileName = False
230			haveOutputFileName = False
231			doEinstein = False
232
233			try:
234			opts, args = getopt.getopt(argv, "hgesf:o:", ["help", "einstein", "stat-file=", "output-file="])
235			except getopt.GetoptError:
236			usage()
237			sys.exit(2)
238			for opt, arg in opts:
239			if opt in ("-h", "--help"):
240			usage()
241			sys.exit()
242			elif opt in ("-e", "--einstein"):
243			doEinstein = True
244			elif opt in ("-f", "--stat-file"):
245			statFileName = arg
246			haveStatFileName = True
247			elif opt in ("-o", "--output-file"):
248			outputFileName = arg
249			haveOutputFileName = True
250			if (not haveStatFileName):
251			usage()
252			print "No stat file was specified"
253			sys.exit()
254			if (not haveOutputFileName):
255			usage()
256			print "No output file was specified"
257			sys.exit()
258
259			readStatFile(statFileName);
260			computeAverages();
261			computeCorrelations(outputFileName);
262
263			if __name__ == "__main__":
264			if len(sys.argv) == 1:
265			usage()
266			sys.exit()
267			main(sys.argv[1:])