dump.py
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Created: Wed, Nov 20, 16:30

dump.py
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	# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
	# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
	#
	# Copyright (2005) Sandia Corporation. Under the terms of Contract
	# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
	# certain rights in this software. This software is distributed under
	# the GNU General Public License.

	# for python3 compatibility

	from __future__ import print_function

	# dump tool

	oneline = "Read, write, manipulate dump files and particle attributes"

	docstr = """
	d = dump("dump.one") read in one or more dump files
	d = dump("dump.1 dump.2.gz") can be gzipped
	d = dump("dump.*") wildcard expands to multiple files
	d = dump("dump.*",0) two args = store filenames, but don't read

	incomplete and duplicate snapshots are deleted
	if atoms have 5 or 8 columns, assign id,type,x,y,z (ix,iy,iz)
	atoms will be unscaled if stored in files as scaled

	time = d.next() read next snapshot from dump files

	used with 2-argument constructor to allow reading snapshots one-at-a-time
	snapshot will be skipped only if another snapshot has same time stamp
	return time stamp of snapshot read
	return -1 if no snapshots left or last snapshot is incomplete
	no column name assignment or unscaling is performed

	d.map(1,"id",3,"x") assign names to atom columns (1-N)

	not needed if dump file is self-describing

	d.tselect.all() select all timesteps
	d.tselect.one(N) select only timestep N
	d.tselect.none() deselect all timesteps
	d.tselect.skip(M) select every Mth step
	d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps
	d.delete() delete non-selected timesteps

	selecting a timestep also selects all atoms in the timestep
	skip() and test() only select from currently selected timesteps
	test() uses a Python Boolean expression with $t for timestep value
	Python comparison syntax: == != < > <= >= and or

	d.aselect.all() select all atoms in all steps
	d.aselect.all(N) select all atoms in one step
	d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps
	d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step

	all() with no args selects atoms from currently selected timesteps
	test() with one arg selects atoms from currently selected timesteps
	test() sub-selects from currently selected atoms
	test() uses a Python Boolean expression with $ for atom attributes
	Python comparison syntax: == != < > <= >= and or
	$name must end with a space

	d.write("file") write selected steps/atoms to dump file
	d.write("file",head,app) write selected steps/atoms to dump file
	d.scatter("tmp") write selected steps/atoms to multiple files

	write() can be specified with 2 additional flags
	headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
	scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc

	d.scale() scale x,y,z to 0-1 for all timesteps
	d.scale(100) scale atom coords for timestep N
	d.unscale() unscale x,y,z to box size to all timesteps
	d.unscale(1000) unscale atom coords for timestep N
	d.wrap() wrap x,y,z into periodic box via ix,iy,iz
	d.unwrap() unwrap x,y,z out of box via ix,iy,iz
	d.owrap("other") wrap x,y,z to same image as another atom
	d.sort() sort atoms by atom ID in all selected steps
	d.sort("x") sort atoms by column value in all steps
	d.sort(1000) sort atoms in timestep N

	scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
	wrap(), unwrap(), owrap() require ix,iy,iz be defined
	owrap() requires a column be defined which contains an atom ID
	name of that column is the argument to owrap()
	x,y,z for each atom is wrapped to same image as the associated atom ID
	useful for wrapping all molecule's atoms the same so it is contiguous

	m1,m2 = d.minmax("type") find min/max values for a column
	d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value
	d.setv("type",vector) set a column to a vector of values
	d.spread("ke",N,"color") 2nd col = N ints spread over 1st col
	d.clone(1000,"color") clone timestep N values to other steps

	minmax() operates on selected timesteps and atoms
	set() operates on selected timesteps and atoms
	left hand side column is created if necessary
	left-hand side column is unset or unchanged for non-selected atoms
	equation is in Python syntax
	use $ for column names, $name must end with a space
	setv() operates on selected timesteps and atoms
	if column label does not exist, column is created
	values in vector are assigned sequentially to atoms, so may want to sort()
	length of vector must match # of selected atoms
	spread() operates on selected timesteps and atoms
	min and max are found for 1st specified column across all selected atoms
	atom's value is linear mapping (1-N) between min and max
	that is stored in 2nd column (created if needed)
	useful for creating a color map
	clone() operates on selected timesteps and atoms
	values at every timestep are set to value at timestep N for that atom ID
	useful for propagating a color map

	t = d.time() return vector of selected timestep values
	fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N
	fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N

	atom() returns vectors with one value for each selected timestep
	vecs() returns vectors with one value for each selected atom in the timestep

	index,time,flag = d.iterator(0/1) loop over dump snapshots
	time,box,atoms,bonds,tris = d.viz(index) return list of viz objects
	d.atype = "color" set column returned as "type" by viz
	d.extra("dump.bond") read bond list from dump file
	d.extra(data) extract bond/tri/line list from data

	iterator() loops over selected timesteps
	iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
	index = index within dump object (0 to # of snapshots)
	time = timestep value
	flag = -1 when iteration is done, 1 otherwise
	viz() returns info for selected atoms for specified timestep index
	time = timestep value
	box = [xlo,ylo,zlo,xhi,yhi,zhi]
	atoms = id,type,x,y,z for each atom as 2d array
	bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array
	if bonds() was used to define bonds, else empty list
	tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array
	if extra() was used to define tris, else empty list
	lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
	if extra() was used to define lines, else empty list
	atype is column name viz() will return as atom type (def = "type")
	extra() stores list of bonds/tris/lines to return each time viz() is called
	"""

	# History
	# 8/05, Steve Plimpton (SNL): original version
	# 12/09, David Hart (SNL): allow use of NumPy or Numeric

	# ToDo list
	# try to optimize this line in read_snap: words += f.readline().split()
	# allow $name in aselect.test() and set() to end with non-space
	# should next() snapshot be auto-unscaled ?

	# Variables
	# flist = list of dump file names
	# increment = 1 if reading snapshots one-at-a-time
	# nextfile = which file to read from via next()
	# eof = ptr into current file for where to read via next()
	# nsnaps = # of snapshots
	# nselect = # of selected snapshots
	# snaps = list of snapshots
	# names = dictionary of column names:
	# key = "id", value = column # (0 to M-1)
	# tselect = class for time selection
	# aselect = class for atom selection
	# atype = name of vector used as atom type by viz extract
	# bondflag = 0 if no bonds, 1 if they are defined statically
	# bondlist = static list of bonds to viz() return for all snapshots
	# only a list of atom pairs, coords have to be created for each snapshot
	# triflag = 0 if no tris, 1 if they are defined statically, 2 if dynamic
	# trilist = static list of tris to return via viz() for all snapshots
	# lineflag = 0 if no lines, 1 if they are defined statically
	# linelist = static list of lines to return via viz() for all snapshots
	# Snap = one snapshot
	# time = time stamp
	# tselect = 0/1 if this snapshot selected
	# natoms = # of atoms
	# nselect = # of selected atoms in this snapshot
	# aselect[i] = 0/1 for each atom
	# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
	# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1

	# Imports and external programs

	import sys, re, glob, types
	from os import popen
	from math import * # any function could be used by set()

	try:
	import numpy as np
	oldnumeric = False
	except:
	import Numeric as np
	oldnumeric = True

	try: from DEFAULTS import PIZZA_GUNZIP
	except: PIZZA_GUNZIP = "gunzip"

	# Class definition

	class dump:

	# --------------------------------------------------------------------

	def __init__(self,*list):
	self.snaps = []
	self.nsnaps = self.nselect = 0
	self.names = {}
	self.tselect = tselect(self)
	self.aselect = aselect(self)
	self.atype = "type"
	self.bondflag = 0
	self.bondlist = []
	self.triflag = 0
	self.trilist = []
	self.triobj = 0
	self.lineflag = 0
	self.linelist = []

	# flist = list of all dump file names

	words = list[0].split()
	self.flist = []
	for word in words: self.flist += glob.glob(word)
	if len(self.flist) == 0 and len(list) == 1:
	raise StandardError("no dump file specified")

	if len(list) == 1:
	self.increment = 0
	self.read_all()
	else:
	self.increment = 1
	self.nextfile = 0
	self.eof = 0

	# --------------------------------------------------------------------

	def read_all(self):

	# read all snapshots from each file
	# test for gzipped files

	for file in self.flist:
	if file[-3:] == ".gz":
	f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
	else: f = open(file)

	snap = self.read_snapshot(f)
	while snap:
	self.snaps.append(snap)
	print(snap.time,end='')
	sys.stdout.flush()
	snap = self.read_snapshot(f)

	f.close()
	print()

	# sort entries by timestep, cull duplicates

	self.snaps.sort(self.compare_time)
	self.cull()
	self.nsnaps = len(self.snaps)
	print("read %d snapshots" % self.nsnaps)

	# select all timesteps and atoms

	self.tselect.all()

	# set default names for atom columns if file wasn't self-describing

	if len(self.snaps) == 0:
	print("no column assignments made")
	elif len(self.names):
	print("assigned columns:",self.names2str())
	elif self.snaps[0].atoms == None:
	print("no column assignments made")
	elif len(self.snaps[0].atoms[0]) == 5:
	self.map(1,"id",2,"type",3,"x",4,"y",5,"z")
	print("assigned columns:",self.names2str())
	elif len(self.snaps[0].atoms[0]) == 8:
	self.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"ix",7,"iy",8,"iz")
	print("assigned columns:",self.names2str())
	else:
	print("no column assignments made")

	# if snapshots are scaled, unscale them

	if (not self.names.has_key("x")) or \
	(not self.names.has_key("y")) or \
	(not self.names.has_key("z")):
	print("no unscaling could be performed")
	elif self.nsnaps > 0:
	if self.scaled(self.nsnaps-1): self.unscale()
	else: print("dump is already unscaled")

	# --------------------------------------------------------------------
	# read next snapshot from list of files

	def next(self):

	if not self.increment: raise StandardError("cannot read incrementally")

	# read next snapshot in current file using eof as pointer
	# if fail, try next file
	# if new snapshot time stamp already exists, read next snapshot

	while 1:
	f = open(self.flist[self.nextfile],'rb')
	f.seek(self.eof)
	snap = self.read_snapshot(f)
	if not snap:
	self.nextfile += 1
	if self.nextfile == len(self.flist): return -1
	f.close()
	self.eof = 0
	continue
	self.eof = f.tell()
	f.close()
	try:
	self.findtime(snap.time)
	continue
	except: break

	# select the new snapshot with all its atoms

	self.snaps.append(snap)
	snap = self.snaps[self.nsnaps]
	snap.tselect = 1
	snap.nselect = snap.natoms
	for i in range(snap.natoms): snap.aselect[i] = 1
	self.nsnaps += 1
	self.nselect += 1

	return snap.time

	# --------------------------------------------------------------------
	# read a single snapshot from file f
	# return snapshot or 0 if failed
	# assign column names if not already done and file is self-describing
	# convert xs,xu to x

	def read_snapshot(self,f):
	try:
	snap = Snap()
	item = f.readline()
	snap.time = int(f.readline().split()[0]) # just grab 1st field
	item = f.readline()
	snap.natoms = int(f.readline())

	snap.aselect = np.zeros(snap.natoms)

	item = f.readline()
	words = f.readline().split()
	snap.xlo,snap.xhi = float(words[0]),float(words[1])
	words = f.readline().split()
	snap.ylo,snap.yhi = float(words[0]),float(words[1])
	words = f.readline().split()
	snap.zlo,snap.zhi = float(words[0]),float(words[1])

	item = f.readline()
	if len(self.names) == 0:
	words = item.split()[2:]
	if len(words):
	for i in range(len(words)):
	if words[i] == "xs" or words[i] == "xu":
	self.names["x"] = i
	elif words[i] == "ys" or words[i] == "yu":
	self.names["y"] = i
	elif words[i] == "zs" or words[i] == "zu":
	self.names["z"] = i
	else: self.names[words[i]] = i

	if snap.natoms:
	words = f.readline().split()
	ncol = len(words)
	for i in range(1,snap.natoms):
	words += f.readline().split()
	floats = map(float,words)
	if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
	else: atoms = np.zeros((snap.natoms,ncol),np.float)
	start = 0
	stop = ncol
	for i in range(snap.natoms):
	atoms[i] = floats[start:stop]
	start = stop
	stop += ncol
	else: atoms = None
	snap.atoms = atoms
	return snap
	except:
	return 0

	# --------------------------------------------------------------------
	# decide if snapshot i is scaled/unscaled from coords of first and last atom

	def scaled(self,i):
	ix = self.names["x"]
	iy = self.names["y"]
	iz = self.names["z"]
	natoms = self.snaps[i].natoms
	if natoms == 0: return 0
	x1 = self.snaps[i].atoms[0][ix]
	y1 = self.snaps[i].atoms[0][iy]
	z1 = self.snaps[i].atoms[0][iz]
	x2 = self.snaps[i].atoms[natoms-1][ix]
	y2 = self.snaps[i].atoms[natoms-1][iy]
	z2 = self.snaps[i].atoms[natoms-1][iz]
	if x1 >= -0.1 and x1 <= 1.1 and y1 >= -0.1 and y1 <= 1.1 and \
	z1 >= -0.1 and z1 <= 1.1 and x2 >= -0.1 and x2 <= 1.1 and \
	y2 >= -0.1 and y2 <= 1.1 and z2 >= -0.1 and z2 <= 1.1:
	return 1
	else: return 0

	# --------------------------------------------------------------------
	# map atom column names

	def map(self,*pairs):
	if len(pairs) % 2 != 0:
	raise StandardError("dump map() requires pairs of mappings")
	for i in range(0,len(pairs),2):
	j = i + 1
	self.names[pairs[j]] = pairs[i]-1

	# delete unselected snapshots

	# --------------------------------------------------------------------

	def delete(self):
	ndel = i = 0
	while i < self.nsnaps:
	if not self.snaps[i].tselect:
	del self.snaps[i]
	self.nsnaps -= 1
	ndel += 1
	else: i += 1
	print("%d snapshots deleted" % ndel)
	print("%d snapshots remaining" % self.nsnaps)

	# --------------------------------------------------------------------
	# scale coords to 0-1 for all snapshots or just one

	def scale(self,*list):
	if len(list) == 0:
	print("Scaling dump ...")
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	for snap in self.snaps: self.scale_one(snap,x,y,z)
	else:
	i = self.findtime(list[0])
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	self.scale_one(self.snaps[i],x,y,z)

	# --------------------------------------------------------------------

	def scale_one(self,snap,x,y,z):
	xprdinv = 1.0 / (snap.xhi - snap.xlo)
	yprdinv = 1.0 / (snap.yhi - snap.ylo)
	zprdinv = 1.0 / (snap.zhi - snap.zlo)
	atoms = snap.atoms
	atoms[:,x] = (atoms[:,x] - snap.xlo) * xprdinv
	atoms[:,y] = (atoms[:,y] - snap.ylo) * yprdinv
	atoms[:,z] = (atoms[:,z] - snap.zlo) * zprdinv

	# --------------------------------------------------------------------
	# unscale coords from 0-1 to box size for all snapshots or just one

	def unscale(self,*list):
	if len(list) == 0:
	print("Unscaling dump ...")
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	for snap in self.snaps: self.unscale_one(snap,x,y,z)
	else:
	i = self.findtime(list[0])
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	self.unscale_one(self.snaps[i],x,y,z)

	# --------------------------------------------------------------------

	def unscale_one(self,snap,x,y,z):
	xprd = snap.xhi - snap.xlo
	yprd = snap.yhi - snap.ylo
	zprd = snap.zhi - snap.zlo
	atoms = snap.atoms
	atoms[:,x] = snap.xlo + atoms[:,x]*xprd
	atoms[:,y] = snap.ylo + atoms[:,y]*yprd
	atoms[:,z] = snap.zlo + atoms[:,z]*zprd

	# --------------------------------------------------------------------
	# wrap coords from outside box to inside

	def wrap(self):
	print("Wrapping dump ...")

	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	ix = self.names["ix"]
	iy = self.names["iy"]
	iz = self.names["iz"]

	for snap in self.snaps:
	xprd = snap.xhi - snap.xlo
	yprd = snap.yhi - snap.ylo
	zprd = snap.zhi - snap.zlo
	atoms = snap.atoms
	atoms[:,x] -= atoms[:,ix]*xprd
	atoms[:,y] -= atoms[:,iy]*yprd
	atoms[:,z] -= atoms[:,iz]*zprd

	# --------------------------------------------------------------------
	# unwrap coords from inside box to outside

	def unwrap(self):
	print("Unwrapping dump ...")

	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	ix = self.names["ix"]
	iy = self.names["iy"]
	iz = self.names["iz"]

	for snap in self.snaps:
	xprd = snap.xhi - snap.xlo
	yprd = snap.yhi - snap.ylo
	zprd = snap.zhi - snap.zlo
	atoms = snap.atoms
	atoms[:,x] += atoms[:,ix]*xprd
	atoms[:,y] += atoms[:,iy]*yprd
	atoms[:,z] += atoms[:,iz]*zprd

	# --------------------------------------------------------------------
	# wrap coords to same image as atom ID stored in "other" column

	def owrap(self,other):
	print("Wrapping to other ...")

	id = self.names["id"]
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]
	ix = self.names["ix"]
	iy = self.names["iy"]
	iz = self.names["iz"]
	iother = self.names[other]

	for snap in self.snaps:
	xprd = snap.xhi - snap.xlo
	yprd = snap.yhi - snap.ylo
	zprd = snap.zhi - snap.zlo
	atoms = snap.atoms
	ids = {}
	for i in range(snap.natoms):
	ids[atoms[i][id]] = i
	for i in range(snap.natoms):
	j = ids[atoms[i][iother]]
	atoms[i][x] += (atoms[i][ix]-atoms[j][ix])*xprd
	atoms[i][y] += (atoms[i][iy]-atoms[j][iy])*yprd
	atoms[i][z] += (atoms[i][iz]-atoms[j][iz])*zprd

	# --------------------------------------------------------------------
	# convert column names assignment to a string, in column order

	def names2str(self):
	ncol = len(self.snaps[0].atoms[0])
	pairs = self.names.items()
	values = self.names.values()
	str = ""
	for i in range(ncol):
	if i in values: str += pairs[values.index(i)][0] + ' '
	return str

	# --------------------------------------------------------------------
	# sort atoms by atom ID in all selected timesteps by default
	# if arg = string, sort all steps by that column
	# if arg = numeric, sort atoms in single step

	def sort(self,*list):
	if len(list) == 0:
	print("Sorting selected snapshots ...")
	id = self.names["id"]
	for snap in self.snaps:
	if snap.tselect: self.sort_one(snap,id)
	elif type(list[0]) is types.StringType:
	print("Sorting selected snapshots by %s ..." % list[0])
	id = self.names[list[0]]
	for snap in self.snaps:
	if snap.tselect: self.sort_one(snap,id)
	else:
	i = self.findtime(list[0])
	id = self.names["id"]
	self.sort_one(self.snaps[i],id)

	# --------------------------------------------------------------------
	# sort a single snapshot by ID column

	def sort_one(self,snap,id):
	atoms = snap.atoms
	ids = atoms[:,id]
	ordering = np.argsort(ids)
	for i in range(len(atoms[0])):
	atoms[:,i] = np.take(atoms[:,i],ordering)

	# --------------------------------------------------------------------
	# write a single dump file from current selection

	def write(self,file,header=1,append=0):
	if len(self.snaps): namestr = self.names2str()
	if not append: f = open(file,"w")
	else: f = open(file,"a")
	for snap in self.snaps:
	if not snap.tselect: continue
	print(snap.time,end='')
	sys.stdout.flush()

	if header:
	print("ITEM: TIMESTEP",file=f)
	print(snap.time,file=f)
	print("ITEM: NUMBER OF ATOMS",file=f)
	print(snap.nselect,file=f)
	print("ITEM: BOX BOUNDS",file=f)
	print(snap.xlo,snap.xhi,file=f)
	print(snap.ylo,snap.yhi,file=f)
	print(snap.zlo,snap.zhi,file=f)
	print("ITEM: ATOMS",namestr,file=f)

	atoms = snap.atoms
	nvalues = len(atoms[0])
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	line = ""
	for j in range(nvalues):
	if (j < 2):
	line += str(int(atoms[i][j])) + " "
	else:
	line += str(atoms[i][j]) + " "
	print(line,file=f)
	f.close()
	print("\n%d snapshots" % self.nselect)

	# --------------------------------------------------------------------
	# write one dump file per snapshot from current selection

	def scatter(self,root):
	if len(self.snaps): namestr = self.names2str()
	for snap in self.snaps:
	if not snap.tselect: continue
	print(snap.time,end='')
	sys.stdout.flush()

	file = root + "." + str(snap.time)
	f = open(file,"w")
	print("ITEM: TIMESTEP",file=f)
	print(snap.time,file=f)
	print("ITEM: NUMBER OF ATOMS",file=f)
	print(snap.nselect,file=f)
	print("ITEM: BOX BOUNDS",file=f)
	print(snap.xlo,snap.xhi,file=f)
	print(snap.ylo,snap.yhi,file=f)
	print(snap.zlo,snap.zhi,file=f)
	print("ITEM: ATOMS",namestr,file=f)

	atoms = snap.atoms
	nvalues = len(atoms[0])
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	line = ""
	for j in range(nvalues):
	if (j < 2):
	line += str(int(atoms[i][j])) + " "
	else:
	line += str(atoms[i][j]) + " "
	print(line,file=f)
	f.close()
	print("\n%d snapshots" % self.nselect)

	# --------------------------------------------------------------------
	# find min/max across all selected snapshots/atoms for a particular column

	def minmax(self,colname):
	icol = self.names[colname]
	min = 1.0e20
	max = -min
	for snap in self.snaps:
	if not snap.tselect: continue
	atoms = snap.atoms
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	if atoms[i][icol] < min: min = atoms[i][icol]
	if atoms[i][icol] > max: max = atoms[i][icol]
	return (min,max)

	# --------------------------------------------------------------------
	# set a column value via an equation for all selected snapshots

	def set(self,eq):
	print("Setting ...")
	pattern = "\$\w*"
	list = re.findall(pattern,eq)

	lhs = list[0][1:]
	if not self.names.has_key(lhs):
	self.newcolumn(lhs)

	for item in list:
	name = item[1:]
	column = self.names[name]
	insert = "snap.atoms[i][%d]" % (column)
	eq = eq.replace(item,insert)
	ceq = compile(eq,'','single')

	for snap in self.snaps:
	if not snap.tselect: continue
	for i in range(snap.natoms):
	if snap.aselect[i]: exec(ceq)

	# --------------------------------------------------------------------
	# set a column value via an input vec for all selected snapshots/atoms

	def setv(self,colname,vec):
	print("Setting ...")
	if not self.names.has_key(colname):
	self.newcolumn(colname)
	icol = self.names[colname]

	for snap in self.snaps:
	if not snap.tselect: continue
	if snap.nselect != len(vec):
	raise StandardError("vec length does not match # of selected atoms")
	atoms = snap.atoms
	m = 0
	for i in range(snap.natoms):
	if snap.aselect[i]:
	atoms[i][icol] = vec[m]
	m += 1

	# --------------------------------------------------------------------
	# clone value in col across selected timesteps for atoms with same ID

	def clone(self,nstep,col):
	istep = self.findtime(nstep)
	icol = self.names[col]
	id = self.names["id"]
	ids = {}
	for i in range(self.snaps[istep].natoms):
	ids[self.snaps[istep].atoms[i][id]] = i
	for snap in self.snaps:
	if not snap.tselect: continue
	atoms = snap.atoms
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	j = ids[atoms[i][id]]
	atoms[i][icol] = self.snaps[istep].atoms[j][icol]

	# --------------------------------------------------------------------
	# values in old column are spread as ints from 1-N and assigned to new column

	def spread(self,old,n,new):
	iold = self.names[old]
	if not self.names.has_key(new): self.newcolumn(new)
	inew = self.names[new]

	min,max = self.minmax(old)
	print("min/max = ",min,max)

	gap = max - min
	invdelta = n/gap
	for snap in self.snaps:
	if not snap.tselect: continue
	atoms = snap.atoms
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	ivalue = int((atoms[i][iold] - min) * invdelta) + 1
	if ivalue > n: ivalue = n
	if ivalue < 1: ivalue = 1
	atoms[i][inew] = ivalue

	# --------------------------------------------------------------------
	# return vector of selected snapshot time stamps

	def time(self):
	vec = self.nselect * [0]
	i = 0
	for snap in self.snaps:
	if not snap.tselect: continue
	vec[i] = snap.time
	i += 1
	return vec

	# --------------------------------------------------------------------
	# extract vector(s) of values for atom ID n at each selected timestep

	def atom(self,n,*list):
	if len(list) == 0:
	raise StandardError("no columns specified")
	columns = []
	values = []
	for name in list:
	columns.append(self.names[name])
	values.append(self.nselect * [0])
	ncol = len(columns)

	id = self.names["id"]
	m = 0
	for snap in self.snaps:
	if not snap.tselect: continue
	atoms = snap.atoms
	for i in range(snap.natoms):
	if atoms[i][id] == n: break
	if atoms[i][id] != n:
	raise StandardError("could not find atom ID in snapshot")
	for j in range(ncol):
	values[j][m] = atoms[i][columns[j]]
	m += 1

	if len(list) == 1: return values[0]
	else: return values

	# --------------------------------------------------------------------
	# extract vector(s) of values for selected atoms at chosen timestep

	def vecs(self,n,*list):
	snap = self.snaps[self.findtime(n)]

	if len(list) == 0:
	raise StandardError("no columns specified")
	columns = []
	values = []
	for name in list:
	columns.append(self.names[name])
	values.append(snap.nselect * [0])
	ncol = len(columns)

	m = 0
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	for j in range(ncol):
	values[j][m] = snap.atoms[i][columns[j]]
	m += 1

	if len(list) == 1: return values[0]
	else: return values

	# --------------------------------------------------------------------
	# add a new column to every snapshot and set value to 0
	# set the name of the column to str

	def newcolumn(self,str):
	ncol = len(self.snaps[0].atoms[0])
	self.map(ncol+1,str)
	for snap in self.snaps:
	atoms = snap.atoms
	if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
	else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
	newatoms[:,0:ncol] = snap.atoms
	snap.atoms = newatoms

	# --------------------------------------------------------------------
	# sort snapshots on time stamp

	def compare_time(self,a,b):
	if a.time < b.time:
	return -1
	elif a.time > b.time:
	return 1
	else:
	return 0

	# --------------------------------------------------------------------
	# delete successive snapshots with duplicate time stamp

	def cull(self):
	i = 1
	while i < len(self.snaps):
	if self.snaps[i].time == self.snaps[i-1].time:
	del self.snaps[i]
	else:
	i += 1

	# --------------------------------------------------------------------
	# iterate over selected snapshots

	def iterator(self,flag):
	start = 0
	if flag: start = self.iterate + 1
	for i in range(start,self.nsnaps):
	if self.snaps[i].tselect:
	self.iterate = i
	return i,self.snaps[i].time,1
	return 0,0,-1

	# --------------------------------------------------------------------
	# return list of atoms to viz for snapshot isnap
	# augment with bonds, tris, lines if extra() was invoked

	def viz(self,isnap):
	snap = self.snaps[isnap]

	time = snap.time
	box = [snap.xlo,snap.ylo,snap.zlo,snap.xhi,snap.yhi,snap.zhi]
	id = self.names["id"]
	type = self.names[self.atype]
	x = self.names["x"]
	y = self.names["y"]
	z = self.names["z"]

	# create atom list needed by viz from id,type,x,y,z
	# need Numeric/Numpy mode here

	atoms = []
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	atom = snap.atoms[i]
	atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]])

	# create list of current bond coords from static bondlist
	# alist = dictionary of atom IDs for atoms list
	# lookup bond atom IDs in alist and grab their coords
	# try is used since some atoms may be unselected
	# any bond with unselected atom is not returned to viz caller
	# need Numeric/Numpy mode here

	bonds = []
	if self.bondflag:
	alist = {}
	for i in range(len(atoms)): alist[int(atoms[i][0])] = i
	for bond in self.bondlist:
	try:
	i = alist[bond[2]]
	j = alist[bond[3]]
	atom1 = atoms[i]
	atom2 = atoms[j]
	bonds.append([bond[0],bond[1],atom1[2],atom1[3],atom1[4],
	atom2[2],atom2[3],atom2[4],atom1[1],atom2[1]])
	except: continue

	tris = []
	if self.triflag:
	if self.triflag == 1: tris = self.trilist
	elif self.triflag == 2:
	timetmp,boxtmp,atomstmp,bondstmp, \
	tris,linestmp = self.triobj.viz(time,1)

	lines = []
	if self.lineflag: lines = self.linelist

	return time,box,atoms,bonds,tris,lines

	# --------------------------------------------------------------------

	def findtime(self,n):
	for i in range(self.nsnaps):
	if self.snaps[i].time == n: return i
	raise StandardError("no step %d exists" % n)

	# --------------------------------------------------------------------
	# return maximum box size across all selected snapshots

	def maxbox(self):
	xlo = ylo = zlo = None
	xhi = yhi = zhi = None
	for snap in self.snaps:
	if not snap.tselect: continue
	if xlo == None or snap.xlo < xlo: xlo = snap.xlo
	if xhi == None or snap.xhi > xhi: xhi = snap.xhi
	if ylo == None or snap.ylo < ylo: ylo = snap.ylo
	if yhi == None or snap.yhi > yhi: yhi = snap.yhi
	if zlo == None or snap.zlo < zlo: zlo = snap.zlo
	if zhi == None or snap.zhi > zhi: zhi = snap.zhi
	return [xlo,ylo,zlo,xhi,yhi,zhi]

	# --------------------------------------------------------------------
	# return maximum atom type across all selected snapshots and atoms

	def maxtype(self):
	icol = self.names["type"]
	max = 0
	for snap in self.snaps:
	if not snap.tselect: continue
	atoms = snap.atoms
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	if atoms[i][icol] > max: max = atoms[i][icol]
	return int(max)

	# --------------------------------------------------------------------
	# grab bonds/tris/lines from another object

	def extra(self,arg):

	# read bonds from bond dump file

	if type(arg) is types.StringType:
	try:
	f = open(arg,'r')

	item = f.readline()
	time = int(f.readline())
	item = f.readline()
	nbonds = int(f.readline())
	item = f.readline()
	if not re.search("BONDS",item):
	raise StandardError("could not read bonds from dump file")

	words = f.readline().split()
	ncol = len(words)
	for i in range(1,nbonds):
	words += f.readline().split()
	f.close()

	# convert values to int and absolute value since can be negative types

	if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
	else: bondlist = np.zeros((nbonds,4),np.int)
	ints = [abs(int(value)) for value in words]
	start = 0
	stop = 4
	for i in range(nbonds):
	bondlist[i] = ints[start:stop]
	start += ncol
	stop += ncol
	if bondlist:
	self.bondflag = 1
	self.bondlist = bondlist
	except:
	raise StandardError("could not read from bond dump file")

	# request bonds from data object

	elif type(arg) is types.InstanceType and ".data" in str(arg.__class__):
	try:
	bondlist = []
	bondlines = arg.sections["Bonds"]
	for line in bondlines:
	words = line.split()
	bondlist.append([int(words[0]),int(words[1]),
	int(words[2]),int(words[3])])
	if bondlist:
	self.bondflag = 1
	self.bondlist = bondlist
	except:
	raise StandardError("could not extract bonds from data object")

	# request tris/lines from cdata object

	elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
	try:
	tmp,tmp,tmp,tmp,tris,lines = arg.viz(0)
	if tris:
	self.triflag = 1
	self.trilist = tris
	if lines:
	self.lineflag = 1
	self.linelist = lines
	except:
	raise StandardError("could not extract tris/lines from cdata object")

	# request tris from mdump object

	elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
	try:
	self.triflag = 2
	self.triobj = arg
	except:
	raise StandardError("could not extract tris from mdump object")

	else:
	raise StandardError("unrecognized argument to dump.extra()")

	# --------------------------------------------------------------------

	def compare_atom(self,a,b):
	if a[0] < b[0]:
	return -1
	elif a[0] > b[0]:
	return 1
	else:
	return 0

	# --------------------------------------------------------------------
	# one snapshot

	class Snap:
	pass

	# --------------------------------------------------------------------
	# time selection class

	class tselect:

	def __init__(self,data):
	self.data = data

	# --------------------------------------------------------------------

	def all(self):
	data = self.data
	for snap in data.snaps:
	snap.tselect = 1
	data.nselect = len(data.snaps)
	data.aselect.all()
	print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))

	# --------------------------------------------------------------------

	def one(self,n):
	data = self.data
	for snap in data.snaps:
	snap.tselect = 0
	i = data.findtime(n)
	data.snaps[i].tselect = 1
	data.nselect = 1
	data.aselect.all()
	print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))

	# --------------------------------------------------------------------

	def none(self):
	data = self.data
	for snap in data.snaps:
	snap.tselect = 0
	data.nselect = 0
	print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))

	# --------------------------------------------------------------------

	def skip(self,n):
	data = self.data
	count = n-1
	for snap in data.snaps:
	if not snap.tselect: continue
	count += 1
	if count == n:
	count = 0
	continue
	snap.tselect = 0
	data.nselect -= 1
	data.aselect.all()
	print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))

	# --------------------------------------------------------------------

	def test(self,teststr):
	data = self.data
	snaps = data.snaps
	cmd = "flag = " + teststr.replace("$t","snaps[i].time")
	ccmd = compile(cmd,'','single')
	for i in range(data.nsnaps):
	if not snaps[i].tselect: continue
	exec(ccmd)
	if not flag:
	snaps[i].tselect = 0
	data.nselect -= 1
	data.aselect.all()
	print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))

	# --------------------------------------------------------------------
	# atom selection class

	class aselect:

	def __init__(self,data):
	self.data = data

	# --------------------------------------------------------------------

	def all(self,*args):
	data = self.data
	if len(args) == 0: # all selected timesteps
	for snap in data.snaps:
	if not snap.tselect: continue
	for i in range(snap.natoms): snap.aselect[i] = 1
	snap.nselect = snap.natoms
	else: # one timestep
	n = data.findtime(args[0])
	snap = data.snaps[n]
	for i in range(snap.natoms): snap.aselect[i] = 1
	snap.nselect = snap.natoms

	# --------------------------------------------------------------------

	def test(self,teststr,*args):
	data = self.data

	# replace all $var with snap.atoms references and compile test string

	pattern = "\$\w*"
	list = re.findall(pattern,teststr)
	for item in list:
	name = item[1:]
	column = data.names[name]
	insert = "snap.atoms[i][%d]" % column
	teststr = teststr.replace(item,insert)
	cmd = "flag = " + teststr
	ccmd = compile(cmd,'','single')

	if len(args) == 0: # all selected timesteps
	for snap in data.snaps:
	if not snap.tselect: continue
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	exec(ccmd)
	if not flag:
	snap.aselect[i] = 0
	snap.nselect -= 1
	for i in range(data.nsnaps):
	if data.snaps[i].tselect:
	print("%d atoms of %d selected in first step %d" % \
	(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
	break
	for i in range(data.nsnaps-1,-1,-1):
	if data.snaps[i].tselect:
	print("%d atoms of %d selected in last step %d" % \
	(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
	break

	else: # one timestep
	n = data.findtime(args[0])
	snap = data.snaps[n]
	for i in range(snap.natoms):
	if not snap.aselect[i]: continue
	exec(ccmd)
	if not flag:
	snap.aselect[i] = 0
	snap.nselect -= 1

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