| [e1a46d] | 1 | #!@PYTHON@
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| 2 | #
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| 3 | # calculates xray spectra for each time step with coordinates from PDB
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| 4 |
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| 5 | import sys, os
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| 6 |
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| 7 | exec_prefix="@prefix@"
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| 8 | DATABASE=exec_prefix+"/bin/elements.db" # contains atomic numbers
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| 9 | XRAY="/media/WORK/tmp/CODICE/XR_Intensity"
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| 10 | PYXPLOT="/home/heber/build/pyxplot/pyxplot"
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| 11 | NAME="ettringite_6Gpa"
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| 12 |
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| 13 | # get command line parameters
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| 14 | if (len(sys.argv)) < 5:
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| 15 | print "Usage: "+sys.argv[0]+" <dir> <prefix> <offsetElement> <offsetXYZ> [start from step]"
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| 16 | sys.exit(1)
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| 17 | else:
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| 18 | dir=sys.argv[1]
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| 19 | prefix=sys.argv[2]
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| 20 | offsetElement=int(sys.argv[3])
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| 21 | offsetXYZ=int(sys.argv[4])
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| 22 |
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| 23 | # generate hash map: element -> atomic number
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| 24 | atomic={}
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| 25 | input = open(DATABASE,"r")
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| 26 | for line in input:
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| 27 | if "#" in line:
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| 28 | continue
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| 29 | entries=line.split()
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| 30 | element=entries[1].upper()
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| 31 | number=int(entries[5])
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| 32 | print "Putting "+element+" -> "+str(number)+" into hash map."
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| 33 | atomic[element]=number
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| 34 | input.close()
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| 35 |
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| 36 | # parse each PDB
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| 37 | if (len(sys.argv))>=5:
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| 38 | step=int(sys.argv[5])
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| 39 | else:
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| 40 | step=0
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| 41 | file=dir+"/"+prefix+("%04d" % (step))+".pdb"
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| 42 | while 1:
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| 43 | try:
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| 44 | input=open(file, "r")
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| 45 | except IOError:
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| 46 | print file+" is not found, breaking."
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| 47 | break
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| 48 | print "Current step is "+str(step)+"."
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| 49 | # recode pdb to "Symbol atomicnumber X Y Z" structure
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| 50 | output = open(NAME,"w")
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| 51 | n=0
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| 52 | for line in input:
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| 53 | if "#" in line or "CONECT" in line or "MASTER" in line or "AUTHOR" in line or "COMPND" in line:
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| 54 | continue
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| 55 | if "END" in line:
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| 56 | break
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| 57 | entries=line.split()
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| 58 | try:
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| 59 | element=entries[offsetElement]
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| 60 | except IndexError:
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| 61 | print "Could not read element nr."+str(offsetElement)+" in line: "+line+"."
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| 62 | continue
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| 63 | number=atomic.get(element.upper(), None)
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| 64 | if number != None:
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| 65 | output.write("%s\t%d\t%s\t%s\t%s\n" % (element, int(number), entries[offsetXYZ], entries[offsetXYZ+1], entries[offsetXYZ+2]))
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| 66 | n=n+1
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| 67 | else:
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| 68 | print "WARNING: atomic number for element "+element+" is not known."
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| 69 | output.close()
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| 70 | # call Xray
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| 71 | outputname=dir+"/xray_intensity"+("%04d" % (step))
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| 72 | os.system(XRAY+' '+str(n)+' >'+outputname+'.csv')
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| 73 | # make plotfile and move eps into place
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| 74 | os.system('/bin/cp -f '+outputname+'.csv C3S_xray_spectrum.csv')
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| 75 | os.system(PYXPLOT+' xray_spectrum.pyx')
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| 76 | os.system('/bin/mv C3S_xray_spectrum.eps '+outputname+'.eps')
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| 77 | # next file
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| 78 | step+=1
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| 79 | file=dir+"/"+prefix+("%04d" % (step))+".pdb"
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| 80 |
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| 81 | sys.exit(1)
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