allow selecting a list of timesteps. avoid redundant code
This commit is contained in:
Axel Kohlmeyer
@ -16,15 +16,15 @@ oneline = "Read, write, manipulate dump files and particle attributes"
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docstr = """
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d = dump("dump.one") read in one or more dump files
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d = dump("dump.1 dump.2.gz") can be gzipped
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d = dump("dump.*") wildcard expands to multiple files
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d = dump("dump.*",0) two args = store filenames, but don't read
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d = dump("dump.1 dump.2.gz") can be gzipped
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d = dump("dump.*") wildcard expands to multiple files
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d = dump("dump.*",0) two args = store filenames, but don't read
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incomplete and duplicate snapshots are deleted
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if atoms have 5 or 8 columns, assign id,type,x,y,z (ix,iy,iz)
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atoms will be unscaled if stored in files as scaled
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time = d.next() read next snapshot from dump files
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time = d.next() read next snapshot from dump files
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used with 2-argument constructor to allow reading snapshots one-at-a-time
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snapshot will be skipped only if another snapshot has same time stamp
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@ -36,20 +36,21 @@ d.map(1,"id",3,"x") assign names to atom columns (1-N)
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not needed if dump file is self-describing
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d.tselect.all() select all timesteps
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d.tselect.one(N) select only timestep N
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d.tselect.none() deselect all timesteps
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d.tselect.skip(M) select every Mth step
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d.tselect.all() select all timesteps
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d.tselect.one(N) select only timestep N
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d.tselect.one(N1,N2,N3) select only timestep N1,N2,N3
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d.tselect.none() deselect all timesteps
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d.tselect.skip(M) select every Mth step
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d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps
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d.delete() delete non-selected timesteps
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d.delete() delete non-selected timesteps
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selecting a timestep also selects all atoms in the timestep
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skip() and test() only select from currently selected timesteps
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test() uses a Python Boolean expression with $t for timestep value
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Python comparison syntax: == != < > <= >= and or
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d.aselect.all() select all atoms in all steps
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d.aselect.all(N) select all atoms in one step
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d.aselect.all() select all atoms in all steps
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d.aselect.all(N) select all atoms in one step
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d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps
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d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step
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@ -60,24 +61,24 @@ d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step
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Python comparison syntax: == != < > <= >= and or
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$name must end with a space
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d.write("file") write selected steps/atoms to dump file
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d.write("file",head,app) write selected steps/atoms to dump file
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d.scatter("tmp") write selected steps/atoms to multiple files
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d.write("file") write selected steps/atoms to dump file
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d.write("file",head,app) write selected steps/atoms to dump file
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d.scatter("tmp") write selected steps/atoms to multiple files
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write() can be specified with 2 additional flags
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headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
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scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc
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d.scale() scale x,y,z to 0-1 for all timesteps
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d.scale(100) scale atom coords for timestep N
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d.unscale() unscale x,y,z to box size to all timesteps
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d.unscale(1000) unscale atom coords for timestep N
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d.wrap() wrap x,y,z into periodic box via ix,iy,iz
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d.unwrap() unwrap x,y,z out of box via ix,iy,iz
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d.owrap("other") wrap x,y,z to same image as another atom
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d.sort() sort atoms by atom ID in all selected steps
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d.sort("x") sort atoms by column value in all steps
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d.sort(1000) sort atoms in timestep N
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d.scale() scale x,y,z to 0-1 for all timesteps
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d.scale(100) scale atom coords for timestep N
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d.unscale() unscale x,y,z to box size to all timesteps
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d.unscale(1000) unscale atom coords for timestep N
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d.wrap() wrap x,y,z into periodic box via ix,iy,iz
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d.unwrap() unwrap x,y,z out of box via ix,iy,iz
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d.owrap("other") wrap x,y,z to same image as another atom
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d.sort() sort atoms by atom ID in all selected steps
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d.sort("x") sort atoms by column value in all steps
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d.sort(1000) sort atoms in timestep N
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scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
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wrap(), unwrap(), owrap() require ix,iy,iz be defined
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@ -89,8 +90,8 @@ d.sort(1000) sort atoms in timestep N
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m1,m2 = d.minmax("type") find min/max values for a column
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d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value
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d.setv("type",vector) set a column to a vector of values
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d.spread("ke",N,"color") 2nd col = N ints spread over 1st col
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d.clone(1000,"color") clone timestep N values to other steps
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d.spread("ke",N,"color") 2nd col = N ints spread over 1st col
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d.clone(1000,"color") clone timestep N values to other steps
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minmax() operates on selected timesteps and atoms
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set() operates on selected timesteps and atoms
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@ -111,7 +112,7 @@ d.clone(1000,"color") clone timestep N values to other steps
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values at every timestep are set to value at timestep N for that atom ID
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useful for propagating a color map
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t = d.time() return vector of selected timestep values
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t = d.time() return vector of selected timestep values
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fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N
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fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N
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@ -121,8 +122,8 @@ fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N
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index,time,flag = d.iterator(0/1) loop over dump snapshots
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time,box,atoms,bonds,tris = d.viz(index) return list of viz objects
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d.atype = "color" set column returned as "type" by viz
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d.extra("dump.bond") read bond list from dump file
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d.extra(data) extract bond/tri/line list from data
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d.extra("dump.bond") read bond list from dump file
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d.extra(data) extract bond/tri/line list from data
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iterator() loops over selected timesteps
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iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
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@ -1117,24 +1118,23 @@ class tselect:
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# --------------------------------------------------------------------
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def one(self,n):
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def one(self,*steps):
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data = self.data
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data.nselect = 0
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for snap in data.snaps:
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snap.tselect = 0
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i = data.findtime(n)
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data.snaps[i].tselect = 1
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data.nselect = 1
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data.aselect.all()
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for n in steps:
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i = data.findtime(n)
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data.snaps[i].tselect = 1
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data.nselect += 1
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data.aselect.all()
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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# --------------------------------------------------------------------
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def none(self):
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data = self.data
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for snap in data.snaps:
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snap.tselect = 0
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data.nselect = 0
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print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
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self.one()
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# --------------------------------------------------------------------
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