stat2pcorr

#!@Python3_EXECUTABLE@
"""Pressure Correlation function
 
Computes various correlation functions of the pressure 
that have been stored in a stat file.
 
Usage: stat2pcorr 
 
Options:
  -h, --help              show this help
  -f, --stat-file=...     use specified stat file
  -o, --output-file=...   use specified output (.pcorr) file
 
The script will compute: <(P(t)-<P>)*(P(0)-<P>)> / < (P(0) - <P>)^2 >
 
Example:
   stat2pcorr -f ring5.stat -o ring5.pcorr
 
"""
 
__author__ = "Dan Gezelter (gezelter@nd.edu)"
__version__ = "$Revision$"
__date__ = "$Date$"
 
__copyright__ = "Copyright (c) 2004-present The University of Notre Dame. All Rights Reserved."
__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
    time = []
    temperature = []
    pressure = []
    volume = []
 
    statFile = open(statFileName, 'r')
 
    print("reading File")
    pressSum = 0.0
    volSum = 0.0
    tempSum = 0.0
    
    line = statFile.readline()
    while ("#" in line):
        line = statFile.readline()
 
    while True:
        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]))
                
        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
    
    # Boltzmann's constant amu*Ang^2*fs^-2/K
    kB = 8.31451e-7
        
    if doCorrelation:
        Pcorr = []
        print("computing Pressure Correlation Function")        
        # i corresponds to dt
        for i in range(len(time)):
            # j is the starting time for the correlation
            pp = 0.0
            for j in range( len(time) - i ):
                deltaP1 = pressure[j] - pressAve
                deltaP2 = pressure[j+i] - pressAve
                pp = pp + deltaP1*deltaP2
 
            Pcorr.append(pp / float(len(time) - i))
 
    outputFile = open(outputFileName, 'w')
    for i in range(len(time)):
        if doCorrelation:
            outputFile.write("%f\t%13e\n" % (time[i], Pcorr[i] / Pcorr[0]))
            
    outputFile.close()
 
def main(argv):
    global doCorrelation
    global haveStatFileName
    global haveOutputFileName
    
    haveStatFileName = False
    haveOutputFileName = False
    doCorrelation = True
 
    try:                                
        opts, args = getopt.getopt(argv, "hf:o:", ["help", "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 ("-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:])