--- /home/sjplimp/oldpizza/src/dump.py	2005-09-07 10:13:09.000000000 -0600
+++ /home/sjplimp/pizza/src/dump.py	2005-10-18 08:50:17.000000000 -0600
@@ -106,8 +106,8 @@
 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.bonds("dump.bond")	    		   read bond list from dump file
-d.bonds(data)				   extract bond list from data object
+d.extra("dump.bond")	    		   read bond list from dump file
+d.extra(data)				   extract bond/tri list from data
 
   iterator() loops over selected timesteps
   iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
@@ -118,11 +118,12 @@
     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,z1,t1,t2 for each bond 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 = empty list of triangles
+    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
   atype is column name viz() will return as atom type (def = "type")
-  bonds() stores list of bonds to return each time viz() is called
+  extra() stores list of bonds/tris to return each time viz() is called
 """
 
 # History
@@ -149,7 +150,10 @@
 #   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
-#   bondlist = list of bonds for all snapshots [(id,type,atom1,atom2),...]
+#   bondlist = 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
+#   trilist = list of tris to viz() return for all snapshots
 #   Snap = one snapshot
 #     time = time stamp
 #     tselect = 0/1 if this snapshot selected
@@ -164,6 +168,7 @@
 import sys, commands, re, glob, types
 from os import popen
 from math import *             # any function could be used by set()
+from copy import deepcopy
 import Numeric
 
 try: from DEFAULTS import PIZZA_GUNZIP
@@ -184,6 +189,8 @@
     self.atype = "type"
     self.bondflag = 0
     self.bondlist = []
+    self.triflag = 0
+    self.trilist = []
 
     # flist = list of all dump file names
 
@@ -819,18 +826,17 @@
       atom = snap.atoms[i]
       atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]])
 
-    # need Numeric mode here
     # create list of current bond coords from static bondlist
     # alist = dictionary of atom IDs for atoms list
-    # lookup bond atom IDs in alist
-    # try is used since some may not be there (due to atom selection)
-    #   those bonds are not returned to viz caller
+    # 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 mode here
 
     bonds = []
     if self.bondflag:
       alist = {}
-      for i in xrange(len(atoms)):
-        alist[int(atoms[i][0])] = i
+      for i in xrange(len(atoms)): alist[int(atoms[i][0])] = i
       for one in self.bondlist:
         try:
           i = alist[abs(int(one[2]))]
@@ -841,7 +847,8 @@
                         atom2[2],atom2[3],atom2[4],atom1[1],atom2[1]])
         except: continue
 
-    tris  = []
+    tris = []
+    if self.triflag: tris = deepcopy(self.trilist)
 
     return time,box,atoms,bonds,tris
   
@@ -869,12 +876,10 @@
     return [xlo,ylo,zlo,xhi,yhi,zhi]
   
   # --------------------------------------------------------------------
-  # build static bondlist from dump file or data file
-
-  def bonds(self,arg):
-    self.bondflag = 1
+  # grab bonds/tris from a bond dump file or data file
 
-    if type(arg) is types.StringType:      # read bonds from a dump file
+  def extra(self,arg):
+    if type(arg) is types.StringType:      # read bonds from bond dump file
       try:
         f = open(arg,'r')
 
@@ -900,21 +905,28 @@
           bondlist[i] = [i+1] + ints[start:stop]
           start += ncol
           stop += ncol
+        self.bondflag = 1
+        self.bondlist = bondlist
       except:
         raise StandardError, "could not read bonds from dump file"
 
-    else:                                   # grab bonds from data object
-      try:
+    else:
+      try:                                      # grab bonds from data object
         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])])
+        self.bondflag = 1
+        self.bondlist = bondlist
       except:
-        raise StandardError, "could not extract bonds from data object"
-
-    self.bondlist = bondlist
+        try:                                    # grab tris from cdata object
+          tmp,tmp,tmp,tmp,trilist = arg.viz(0)
+          self.triflag = 1
+          self.trilist = trilist
+        except:
+          raise StandardError,"could not extract bonds/tris from data object"
     
   # --------------------------------------------------------------------