mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4988 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
7e8eb70e44
commit
53c01eb323
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#!/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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#!/usr/local/bin/python
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# combine final snapshots from multiple NEB dump files into 1 dump file
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# Syntax: neb2.py dfinal dfile1 dfile2 ...
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# dfinal = new combined dump file
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# dfile1, dfile2, ... = NEB output dump files from each replica,
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# in correct order
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# for M replicas, final snapshots are renumbered in final file from 1 to M
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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: neb2.py dfinal dfile1 dfile2 ..."
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sys.exit()
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dfinal = sys.argv[1]
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files = sys.argv[2:]
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if os.path.exists(dfinal): os.remove(dfinal)
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n = 1
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for file in files:
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one = dump(file)
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t = one.time()
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one.tselect.one(t[-1])
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one.snaps[-1].time = n
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one.write(dfinal,1,1)
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n += 1
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@ -0,0 +1,88 @@
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#!/usr/local/bin/python
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# make new dump file by combining snapshots from multiple NEB replica dumps
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# Syntax: neb_combine.py -switch arg(s) -switch arg(s) ...
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# -o outfile = new dump file
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# each snapshot has NEB atoms from all replicas
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# -r dump1 dump2 ... = replica dump files of NEB atoms
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# can be in any order
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# -b dumpfile = background atoms (optional)
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# first snapshot in this file used as static non-NEB atoms
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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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# parse args
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outfile = ""
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backfile = ""
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rfiles = []
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argv = sys.argv
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iarg = 1
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narg = len(argv)
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while iarg < narg:
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if argv[iarg] == "-o":
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outfile = argv[iarg+1]
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iarg += 2
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elif argv[iarg] == "-b":
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backfile = argv[iarg+1]
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iarg += 2
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elif argv[iarg] == "-r":
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ilast = iarg + 1
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while ilast < narg and argv[ilast][0] != '-': ilast += 1
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rfiles = argv[iarg+1:ilast]
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iarg = ilast
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else: break
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if iarg < narg or not outfile or not rfiles:
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print "Syntax: neb_combine.py -o outfile -b backfile -r dump1 dump2 ..."
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sys.exit()
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if os.path.exists(outfile): os.remove(outfile)
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# ntotal = total atoms in each snapshot
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# reset IDs of atoms in each NEB dump file
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ntotal = 0
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d = []
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for file in rfiles:
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one = dump(file)
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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 += nnew
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d.append(one)
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# nback = additional atoms in each snapshot
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# reset IDs of atoms in background file
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if backfile:
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back = dump(backfile)
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t = back.time()
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back.tselect.one(t[0])
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nback = back.snaps[0].nselect
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idvec = range(ntotal+1,ntotal+nback+1)
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back.setv("id",idvec)
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else: nback = 0
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ntotal += nback
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# write out each snapshot
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# natoms = ntotal, by overwriting nselect
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# add background atoms if requested
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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(outfile,1,1)
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d[0].snaps[i].nselect = hold
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for one in d[1:]:
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one.tselect.one(time)
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one.write(outfile,0,1)
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if backfile: back.write(outfile,0,1)
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@ -0,0 +1,71 @@
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#!/usr/local/bin/python
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# make new dump file from final snapshots from multiple NEB replica dumps
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# Syntax: neb_final.py -switch arg(s) -switch arg(s) ...
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# -o outfile = new dump file
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# snapshots numbered 1 to M = # of replicas
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# -r dump1 dump2 ... = replica dump files of NEB atoms
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# must be in correct sequence
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# -b dumpfile = background atoms (optional)
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# last snapshot in this file used as static non-NEB atoms
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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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# parse args
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outfile = ""
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backfile = ""
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rfiles = []
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argv = sys.argv
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iarg = 1
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narg = len(argv)
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while iarg < narg:
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if argv[iarg] == "-o":
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outfile = argv[iarg+1]
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iarg += 2
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elif argv[iarg] == "-b":
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backfile = argv[iarg+1]
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iarg += 2
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elif argv[iarg] == "-r":
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ilast = iarg + 1
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while ilast < narg and argv[ilast][0] != '-': ilast += 1
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rfiles = argv[iarg+1:ilast]
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iarg = ilast
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else: break
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if iarg < narg or not outfile or not rfiles:
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print "Syntax: neb_final.py -o outfile -b backfile -r dump1 dump2 ..."
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sys.exit()
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if os.path.exists(outfile): os.remove(outfile)
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# nback = additional atoms in each snapshot
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if backfile:
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back = dump(backfile)
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t = back.time()
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back.tselect.one(t[-1])
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nback = back.snaps[-1].nselect
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else: nback = 0
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# write out each snapshot
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# time = replica #
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# natoms = ntotal, by overwriting nselect
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# add background atoms if requested
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n = 1
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for file in rfiles:
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neb = dump(file)
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t = neb.time()
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neb.tselect.one(t[-1])
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hold = neb.snaps[-1].nselect
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neb.snaps[-1].nselect = hold + nback
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neb.snaps[-1].time = n
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neb.write(outfile,1,1)
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neb.snaps[-1].nselect = hold
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if backfile: back.write(outfile,0,1)
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n += 1
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