make dump.py files consistent and improve python 2/3 portability
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 +36,20 @@ 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.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 $type == 2",N) select matching atoms in one step
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@ -60,24 +60,24 @@ d.aselect.test("$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 +89,8 @@ 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 +111,7 @@ 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 +121,8 @@ 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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@ -148,6 +148,7 @@ d.extra(data) extract bond/tri/line list from data
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# 12/09, David Hart (SNL): allow use of NumPy or Numeric
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# 03/17, Richard Berger (Temple U): improve Python 3 compatibility,
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# simplify read_snapshot by using reshape
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# 08/22, Axel Kohlmeyer (Temple U): remove Numeric, more Python 2/3 compatibility
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# ToDo list
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# try to optimize this line in read_snap: words += f.readline().split()
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@ -261,7 +262,7 @@ class dump:
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snap = self.read_snapshot(f)
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while snap:
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self.snaps.append(snap)
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print(snap.time,end='')
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print(snap.time,end=' ')
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sys.stdout.flush()
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snap = self.read_snapshot(f)
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@ -298,9 +299,9 @@ class dump:
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# if snapshots are scaled, unscale them
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if (not self.names.has_key("x")) or \
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(not self.names.has_key("y")) or \
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(not self.names.has_key("z")):
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if (not "x" in self.names) or \
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(not "y" in self.names) or \
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(not "z" in self.names):
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print("no unscaling could be performed")
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elif self.nsnaps > 0:
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if self.scaled(self.nsnaps-1): self.unscale()
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@ -356,13 +357,13 @@ class dump:
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try:
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snap = Snap()
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item = f.readline()
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snap.time = int(f.readline().decode().split()[0]) # just grab 1st field
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snap.time = int(f.readline().split()[0]) # just grab 1st field
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item = f.readline()
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snap.natoms = int(f.readline().decode())
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snap.natoms = int(f.readline())
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snap.aselect = np.zeros(snap.natoms)
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item = f.readline().decode()
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item = f.readline()
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words = f.readline().split()
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snap.xlo,snap.xhi = float(words[0]),float(words[1])
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words = f.readline().split()
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@ -370,7 +371,7 @@ class dump:
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words = f.readline().split()
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snap.zlo,snap.zhi = float(words[0]),float(words[1])
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item = f.readline().decode()
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item = f.readline()
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if len(self.names) == 0:
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words = item.split()[2:]
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if len(words):
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@ -384,10 +385,10 @@ class dump:
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else: self.names[words[i]] = i
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if snap.natoms:
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words = f.readline().decode().split()
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words = f.readline().split()
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ncol = len(words)
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for i in range(1,snap.natoms):
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words += f.readline().decode().split()
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words += f.readline().split()
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floats = map(float,words)
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atom_data = np.array(list(floats),np.float)
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@ -579,10 +580,10 @@ class dump:
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def names2str(self):
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ncol = len(self.snaps[0].atoms[0])
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pairs = self.names.items()
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values = self.names.values()
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str = ""
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for i in range(ncol):
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if i in values: str += pairs[values.index(i)][0] + ' '
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for p in pairs:
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if p[1] == i: str += p[0] + ' '
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return str
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# --------------------------------------------------------------------
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@ -625,7 +626,7 @@ class dump:
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else: f = open(file,"a")
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for snap in self.snaps:
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if not snap.tselect: continue
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print(snap.time,end='')
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print(snap.time,end=' ')
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sys.stdout.flush()
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if header:
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@ -660,7 +661,7 @@ class dump:
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if len(self.snaps): namestr = self.names2str()
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for snap in self.snaps:
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if not snap.tselect: continue
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print(snap.time,end='')
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print(snap.time,end=' ')
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sys.stdout.flush()
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file = root + "." + str(snap.time)
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@ -714,7 +715,7 @@ class dump:
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list = re.findall(pattern,eq)
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lhs = list[0][1:]
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if not self.names.has_key(lhs):
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if not lhs in self.names:
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self.newcolumn(lhs)
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for item in list:
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@ -734,7 +735,7 @@ class dump:
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def setv(self,colname,vec):
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print("Setting ...")
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if not self.names.has_key(colname):
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if not colname in self.names:
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self.newcolumn(colname)
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icol = self.names[colname]
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@ -772,7 +773,7 @@ class dump:
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def spread(self,old,n,new):
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iold = self.names[old]
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if not self.names.has_key(new): self.newcolumn(new)
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if not new in self.names: self.newcolumn(new)
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inew = self.names[new]
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min,max = self.minmax(old)
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@ -287,7 +287,7 @@ class pdbfile:
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if len(self.files):
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for atom in atoms:
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id = atom[0]
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if self.atomlines.has_key(id):
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if id in self.atomlines:
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(begin,end) = self.atomlines[id]
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line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
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print(line,file=f,end='')
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