56 lines
1.4 KiB
Python
Executable File
56 lines
1.4 KiB
Python
Executable File
#!/usr/local/bin/python
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# combine multiple NEB dump files into 1 dump file
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# Syntax: neb1.py dfinal itype dfile1 dfile2 ...
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# dfinal = new combined dump file
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# itype = atoms of this type are added to each snapshot
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# dfile1, dfile2, ... = NEB output dump files from each replica
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# assumes all N input files have same # of snapshots
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# for each snapshot time:
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# all dfile1 atoms are added to dfinal
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# only atoms of itype in dfile2,...,dfileN are added to dfinal
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import sys,os
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path = os.environ["LAMMPS_PYTHON_TOOLS"]
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sys.path.append(path)
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from dump import dump
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if len(sys.argv) < 5:
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print "Syntax: neb1.py dfinal itype dfile1 dfile2 ..."
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sys.exit()
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dfinal = sys.argv[1]
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itype = int(sys.argv[2])
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files = sys.argv[3:]
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tstr = "$type == %d" % itype
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ntotal = 0
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d = []
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for file in files:
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one = dump(file)
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one.sort()
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if d:
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one.aselect.test(tstr)
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nnew = one.snaps[0].nselect
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idvec = range(ntotal+1,ntotal+nnew+1)
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one.setv("id",idvec)
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ntotal += one.snaps[0].nselect
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d.append(one)
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if os.path.exists(dfinal): os.remove(dfinal)
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times = d[0].time()
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for time in times:
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d[0].tselect.one(time)
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i = d[0].findtime(time)
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hold = d[0].snaps[i].nselect
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d[0].snaps[i].nselect = ntotal
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d[0].write(dfinal,1,1)
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d[0].snaps[i].nselec = hold
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for one in d[1:]:
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one.tselect.one(time)
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one.aselect.test(tstr)
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one.write(dfinal,0,1)
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