mirror of
https://github.com/ParticulateFlow/LPP.git
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98 lines
2.7 KiB
Python
98 lines
2.7 KiB
Python
#!/usr/bin/python
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# Script: density_area.py
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# Purpose: binned atom density by atom type and running area under the curve
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# Syntax: density.py x/y/z nbin outfile files ...
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# x/y/z = get density distribution along this axis
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# nbin = # of bins in desired direction
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# outfile = file to write flux stats to
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# files = series of dump files
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# Example: density_area.py z 100 dens.out dump.*
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# Author: Paul Crozier (Sandia).
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# Modified by Jeff Greathouse (Sandia) to include
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# calculation of area under the curve
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# enable script to run from Python directly w/out Pizza.py
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import sys
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from dump import dump
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if not globals().has_key("argv"): argv = sys.argv
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# main script
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if len(argv) < 5:
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raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..."
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direction = argv[1]
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nbins = int(argv[2])
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outfile = argv[3]
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files = ' '.join(argv[4:])
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# read snapshots one-at-a-time
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d = dump(files,0)
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d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
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first = 1
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nsnaps = 0
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ntypes = 0
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while 1:
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time = d.next()
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if time == -1: break
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if first:
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tmp,ntypes = d.minmax("type")
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ntypes = int(ntypes)
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bin = nbins * [0]
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for i in xrange(nbins): bin[i] = ntypes * [0]
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first = 0
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box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo,
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d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi)
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vol = (box[3] - box[0]) * (box[4] - box[1]) * (box[5] - box[2])
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if direction == "x": type,x = d.vecs(time,"type","x")
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elif direction == "y": type,x = d.vecs(time,"type","y")
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elif direction == "z": type,x = d.vecs(time,"type","z")
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type = map(int,type)
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natoms = len(type)
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for i in xrange(natoms): type[i] -= 1
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for i in xrange(natoms):
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ibin = int(nbins*x[i] + 0.5)
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if (ibin < 0): ibin += nbins
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if (ibin > nbins-1): ibin -= nbins
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bin[ibin][type[i]] += nbins/vol
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nsnaps += 1
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print time,
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print
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print "Printing ",direction,"-directional density distribution in mol/L to", \
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outfile
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conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L
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# Output as x, density_1, area_1, ...
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fp = open(outfile,"w")
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first = 1
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xden = nbins * [0]
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yden = nbins * [0]
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for i in xrange(nbins): yden[i] = ntypes * [0]
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sum = ntypes * [0]
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for i in xrange(nbins):
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xden[i] = float(i)/float(nbins)
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print >>fp, xden[i],
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if first:
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for j in xrange(ntypes):
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yden[i][j] = conversion*bin[i][j]/nsnaps
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print >>fp, yden[i][j], sum[j],
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first = 0
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else:
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for j in xrange(ntypes):
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yden[i][j] = conversion*bin[i][j]/nsnaps
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sum[j] += 0.5 * (xden[i] - xden[i-1]) * (yden[i][j] + yden[i-1][j])
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print >>fp, yden[i][j], sum[j],
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print >>fp
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fp.close()
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