get rid of (evil) tabs and trailing whitespace in bundled Pizza.py components
This commit is contained in:
Axel Kohlmeyer
@ -11,7 +11,7 @@
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oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
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docstr = """
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c = cfg(d) d = object containing atom coords (dump, data)
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c = cfg(d) d = object containing atom coords (dump, data)
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c.one() write all snapshots to tmp.cfg
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c.one("new") write all snapshots to new.cfg
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@ -12,15 +12,15 @@ 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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atoms will be unscaled if stored in files as scaled
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self-describing column names assigned
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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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@ -32,20 +32,20 @@ d.map(1,"id",3,"x") assign names to 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 $type == 2",N) select matching atoms in one step
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@ -56,24 +56,24 @@ d.aselect.test("$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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head = 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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@ -85,8 +85,8 @@ 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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@ -107,17 +107,17 @@ 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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atom() returns vectors with one value for each selected timestep
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vecs() returns vectors with one value for each selected atom in the timestep
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index,time,flag = d.iterator(0/1) loop over dump snapshots
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index,time,flag = d.iterator(0/1) loop over dump snapshots
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time,box,atoms,bonds,tris,lines = 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(obj) extract bond/tri/line info from obj
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d.atype = "color" set column returned as "type" by viz
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d.extra(obj) extract bond/tri/line info from obj
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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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@ -304,15 +304,15 @@ class dump:
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snap = self.read_snapshot(f)
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if not snap:
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self.nextfile += 1
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if self.nextfile == len(self.flist): return -1
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if self.nextfile == len(self.flist): return -1
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f.close()
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self.eof = 0
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continue
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self.eof = 0
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continue
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self.eof = f.tell()
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f.close()
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try:
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self.findtime(snap.time)
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continue
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continue
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except: break
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# select the new snapshot with all its atoms
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@ -11,12 +11,12 @@
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oneline = "Create plots via GnuPlot plotting program"
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docstr = """
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g = gnu() start up GnuPlot
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g.stop() shut down GnuPlot process
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g = gnu() start up GnuPlot
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g.stop() shut down GnuPlot process
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g.plot(a) plot vector A against linear index
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g.plot(a,b) plot B against A
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g.plot(a,b,c,d,...) plot B against A, D against C, etc
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g.plot(a,b) plot B against A
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g.plot(a,b,c,d,...) plot B against A, D against C, etc
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g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
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each plot argument can be a tuple, list, or Numeric/NumPy vector
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@ -29,21 +29,21 @@ g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
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g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
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g.enter() enter GnuPlot shell
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g.enter() enter GnuPlot shell
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gnuplot> plot sin(x) with lines type commands directly to GnuPlot
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gnuplot> exit, quit exit GnuPlot shell
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gnuplot> exit, quit exit GnuPlot shell
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g.export("data",range(100),a,...) create file with columns of numbers
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all vectors must be of equal length
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could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
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g.select(N) figure N becomes the current plot
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g.select(N) figure N becomes the current plot
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subsequent commands apply to this plot
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g.hide(N) delete window for figure N
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g.save("file") save current plot as file.eps
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g.hide(N) delete window for figure N
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g.save("file") save current plot as file.eps
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Set attributes for current plot:
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@ -28,7 +28,7 @@ nvec = l.nvec # of vectors of thermo info
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nlen = l.nlen length of each vectors
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names = l.names list of vector names
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t,pe,... = l.get("Time","KE",...) return one or more vectors of values
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l.write("file.txt") write all vectors to a file
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l.write("file.txt") write all vectors to a file
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l.write("file.txt","Time","PE",...) write listed vectors to a file
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get and write allow abbreviated (uniquely) vector names
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@ -133,9 +133,9 @@ class log:
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else:
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count = 0
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for i in range(self.nvec):
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if self.names[i].find(key) == 0:
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count += 1
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index = i
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if self.names[i].find(key) == 0:
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count += 1
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index = i
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if count == 1:
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map.append(index)
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else:
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@ -161,9 +161,9 @@ class log:
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else:
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count = 0
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for i in range(self.nvec):
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if self.names[i].find(key) == 0:
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count += 1
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index = i
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if self.names[i].find(key) == 0:
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count += 1
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index = i
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if count == 1:
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map.append(index)
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else:
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@ -226,7 +226,7 @@ class log:
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keywords.insert(0,"Step")
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i = 0
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for keyword in keywords:
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self.names.append(keyword)
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self.names.append(keyword)
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self.ptr[keyword] = i
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i += 1
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@ -236,7 +236,7 @@ class log:
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line = txt[s1:s2]
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words = line.split()
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for i in range(len(words)):
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self.names.append(words[i])
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self.names.append(words[i])
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self.ptr[words[i]] = i
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self.nvec = len(self.names)
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@ -275,36 +275,36 @@ class log:
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if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
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if self.style == 2:
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s1 = txt.find("\n",s1) + 1
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s1 = txt.find("\n",s1) + 1
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elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
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s1 = 0
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elif s1 == -1 and s2 >= 0: # found s2, but no s1
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last = 1
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last = 1
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s1 = 0
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elif s1 >= 0 and s2 == -1: # found s1, but no s2
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last = 1
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if self.style == 1:
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s2 = txt.rfind("\n--",s1) + 1
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else:
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s1 = txt.find("\n",s1) + 1
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s1 = txt.find("\n",s1) + 1
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s2 = txt.rfind("\n",s1) + 1
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eof -= len(txt) - s2
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eof -= len(txt) - s2
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elif s1 == -1 and s2 == -1: # found neither
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# could be end-of-file section
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# or entire read was one chunk
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# or entire read was one chunk
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if txt.find("Loop time of",start) == start: # end of file, so exit
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eof -= len(txt) - start # reset eof to "Loop"
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break
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eof -= len(txt) - start # reset eof to "Loop"
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break
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last = 1 # entire read is a chunk
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last = 1 # entire read is a chunk
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s1 = 0
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if self.style == 1:
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s2 = txt.rfind("\n--",s1) + 1
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else:
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s2 = txt.rfind("\n",s1) + 1
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eof -= len(txt) - s2
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if s1 == s2: break
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eof -= len(txt) - s2
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if s1 == s2: break
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chunk = txt[s1:s2-1]
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start = s2
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@ -11,7 +11,7 @@
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oneline = "Convert LAMMPS snapshots to XYZ format"
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docstr = """
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x = xyz(d) d = object containing atom coords (dump, data)
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x = xyz(d) d = object containing atom coords (dump, data)
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x.one() write all snapshots to tmp.xyz
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x.one("new") write all snapshots to new.xyz
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