mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4919 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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b2e57ae886
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@ -56,9 +56,12 @@ 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.scatter("tmp") write selected steps/atoms to mutiple 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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@ -81,6 +84,7 @@ 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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@ -90,6 +94,10 @@ d.clone(1000,"color") clone timestep N values to other steps
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left-hand side column is unset or unchanged for non-selected atoms
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equation is in Python syntax
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use $ for column names, $name must end with a space
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setv() operates on selected timesteps and atoms
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if column label does not exist, column is created
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values in vector are assigned sequentially to atoms, so may want to sort()
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length of vector must match # of selected atoms
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spread() operates on selected timesteps and atoms
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min and max are found for 1st specified column across all selected atoms
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atom's value is linear mapping (1-N) between min and max
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@ -133,6 +141,7 @@ d.extra(data) extract bond/tri/line list from data
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# History
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# 8/05, Steve Plimpton (SNL): original version
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# 12/09, David Hart (SNL): allow use of NumPy or Numeric
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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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@ -173,7 +182,13 @@ d.extra(data) extract bond/tri/line list from data
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import sys, commands, re, glob, types
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from os import popen
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from math import * # any function could be used by set()
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import Numeric
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try:
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import numpy as np
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oldnumeric = False
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except:
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import Numeric as np
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oldnumeric = True
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try: from DEFAULTS import PIZZA_GUNZIP
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except: PIZZA_GUNZIP = "gunzip"
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@ -329,7 +344,7 @@ class dump:
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item = f.readline()
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snap.natoms = int(f.readline())
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snap.aselect = Numeric.zeros(snap.natoms)
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snap.aselect = np.zeros(snap.natoms)
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item = f.readline()
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words = f.readline().split()
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@ -358,7 +373,8 @@ class dump:
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for i in xrange(1,snap.natoms):
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words += f.readline().split()
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floats = map(float,words)
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atoms = Numeric.zeros((snap.natoms,ncol),Numeric.Float)
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if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
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else: atoms = np.zeros((snap.natoms,ncol),np.float)
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start = 0
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stop = ncol
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for i in xrange(snap.natoms):
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@ -585,30 +601,32 @@ class dump:
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def sort_one(self,snap,id):
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atoms = snap.atoms
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ids = atoms[:,id]
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ordering = Numeric.argsort(ids)
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ordering = np.argsort(ids)
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for i in xrange(len(atoms[0])):
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atoms[:,i] = Numeric.take(atoms[:,i],ordering)
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atoms[:,i] = np.take(atoms[:,i],ordering)
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# --------------------------------------------------------------------
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# write a single dump file from current selection
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def write(self,file):
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def write(self,file,header=1,append=0):
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if len(self.snaps): namestr = self.names2str()
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f = open(file,"w")
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if not append: f = open(file,"w")
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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,
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sys.stdout.flush()
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print >>f,"ITEM: TIMESTEP"
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print >>f,snap.time
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print >>f,"ITEM: NUMBER OF ATOMS"
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print >>f,snap.nselect
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print >>f,"ITEM: BOX BOUNDS"
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print >>f,snap.xlo,snap.xhi
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print >>f,snap.ylo,snap.yhi
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print >>f,snap.zlo,snap.zhi
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print >>f,"ITEM: ATOMS",namestr
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if header:
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print >>f,"ITEM: TIMESTEP"
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print >>f,snap.time
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print >>f,"ITEM: NUMBER OF ATOMS"
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print >>f,snap.nselect
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print >>f,"ITEM: BOX BOUNDS"
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print >>f,snap.xlo,snap.xhi
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print >>f,snap.ylo,snap.yhi
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print >>f,snap.zlo,snap.zhi
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print >>f,"ITEM: ATOMS",namestr
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atoms = snap.atoms
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nvalues = len(atoms[0])
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@ -677,7 +695,7 @@ class dump:
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return (min,max)
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# --------------------------------------------------------------------
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# set a column value via an equation
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# set a column value via an equation for all selected snapshots
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def set(self,eq):
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print "Setting ..."
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@ -700,6 +718,26 @@ class dump:
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for i in xrange(snap.natoms):
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if snap.aselect[i]: exec ceq
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# --------------------------------------------------------------------
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# set a column value via an input vec for all selected snapshots/atoms
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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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self.newcolumn(colname)
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icol = self.names[colname]
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for snap in self.snaps:
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if not snap.tselect: continue
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if snap.nselect != len(vec):
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raise StandardError,"vec length does not match # of selected atoms"
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atoms = snap.atoms
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m = 0
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for i in xrange(snap.natoms):
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if snap.aselect[i]:
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atoms[i][icol] = vec[m]
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m += 1
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# --------------------------------------------------------------------
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# clone value in col across selected timesteps for atoms with same ID
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@ -816,7 +854,8 @@ class dump:
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self.map(ncol+1,str)
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for snap in self.snaps:
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atoms = snap.atoms
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newatoms = Numeric.zeros((snap.natoms,ncol+1),Numeric.Float)
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if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
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else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
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newatoms[:,0:ncol] = snap.atoms
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snap.atoms = newatoms
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@ -870,7 +909,7 @@ class dump:
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z = self.names["z"]
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# create atom list needed by viz from id,type,x,y,z
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# need Numeric mode here
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# need Numeric/Numpy mode here
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atoms = []
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for i in xrange(snap.natoms):
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@ -883,7 +922,7 @@ class dump:
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# lookup bond atom IDs in alist and grab their coords
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# try is used since some atoms may be unselected
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# any bond with unselected atom is not returned to viz caller
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# need Numeric mode here
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# need Numeric/Numpy mode here
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bonds = []
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if self.bondflag:
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@ -975,7 +1014,8 @@ class dump:
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# convert values to int and absolute value since can be negative types
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bondlist = Numeric.zeros((nbonds,4),Numeric.Int)
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if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
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else: bondlist = np.zeros((nbonds,4),np.int)
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ints = [abs(int(value)) for value in words]
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start = 0
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stop = 4
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