[Yt-svn] yt-commit r1717 - trunk/yt/lagos

[mturk at wrangler.dreamhost.com]

Author: mturk
Date: Thu May  6 20:35:05 2010
New Revision: 1717
URL: http://yt.enzotools.org/changeset/1717

Log:
Fixing Chombo



Modified:
   trunk/yt/lagos/BaseGridType.py
   trunk/yt/lagos/HierarchyType.py
   trunk/yt/lagos/OutputTypes.py

Modified: trunk/yt/lagos/BaseGridType.py
==============================================================================
--- trunk/yt/lagos/BaseGridType.py	(original)
+++ trunk/yt/lagos/BaseGridType.py	Thu May  6 20:35:05 2010
@@ -662,13 +662,31 @@
 
 class ChomboGrid(AMRGridPatch):
     _id_offset = 0
-    __slots__ = ["_level_id"]
-    def __init__(self, id, hierarchy, level = -1):
+    __slots__ = ["_level_id", "stop_index"]
+    def __init__(self, id, hierarchy, level, start, stop):
         AMRGridPatch.__init__(self, id, filename = hierarchy.hierarchy_filename,
                               hierarchy = hierarchy)
         self.Parent = []
         self.Children = []
         self.Level = level
+        self.start_index = start.copy()#.transpose()
+        self.stop_index = stop.copy()#.transpose()
+        self.ActiveDimensions = stop - start + 1
+
+    def _setup_dx(self):
+        # So first we figure out what the index is.  We don't assume
+        # that dx=dy=dz , at least here.  We probably do elsewhere.
+        id = self.id - self._id_offset
+        if len(self.Parent) > 0:
+            self.dds = self.Parent[0].dds / self.pf["RefineBy"]
+        else:
+            LE, RE = self.hierarchy.grid_left_edge[id,:], \
+                     self.hierarchy.grid_right_edge[id,:]
+            self.dds = na.array((RE-LE)/self.ActiveDimensions)
+        if self.pf["TopGridRank"] < 2: self.dds[1] = 1.0
+        if self.pf["TopGridRank"] < 3: self.dds[2] = 1.0
+        self.data['dx'], self.data['dy'], self.data['dz'] = self.dds
+
 
 class TigerGrid(AMRGridPatch):
     _id_offset = 0

Modified: trunk/yt/lagos/HierarchyType.py
==============================================================================
--- trunk/yt/lagos/HierarchyType.py	(original)
+++ trunk/yt/lagos/HierarchyType.py	Thu May  6 20:35:05 2010
@@ -1285,20 +1285,16 @@
             boxes = f[lev]['boxes'].value
             dx = f[lev].attrs['dx']
             for level_id, box in enumerate(boxes):
-                self.grids.append(self.grid(len(self.grids),self,level=level_number))
+                si = na.array([box['lo_%s' % ax] for ax in 'ijk'])
+                ei = na.array([box['hi_%s' % ax] for ax in 'ijk'])
+                pg = self.grid(len(self.grids),self,level=level_number,
+                               start = si, stop = ei)
+                self.grids.append(pg)
                 self.grids[-1]._level_id = level_id
-                self.grid_left_edge[i] = dx*na.array([box['lo_i'],
-                                                      box['lo_j'],
-                                                      box['lo_k']],
-                                                     dtype=self.float_type)
-                self.grid_right_edge[i] = dx*(na.array([box['hi_i'],
-                                                        box['hi_j'],
-                                                        box['hi_k']],
-                                                       dtype=self.float_type) + 1)
+                self.grid_left_edge[i] = dx*si.astype(self.float_type)
+                self.grid_right_edge[i] = dx*(ei.astype(self.float_type) + 1)
                 self.grid_particle_count[i] = 0
-                self.grid_dimensions[i] = na.array([box['hi_i']-box['lo_i'],
-                                                    box['hi_j']-box['lo_j'],
-                                                    box['hi_k']-box['lo_k']]) + 1
+                self.grid_dimensions[i] = ei - si + 1
                 i += 1
         self.grids = na.array(self.grids, dtype='object')
 

Modified: trunk/yt/lagos/OutputTypes.py
==============================================================================
--- trunk/yt/lagos/OutputTypes.py	(original)
+++ trunk/yt/lagos/OutputTypes.py	Thu May  6 20:35:05 2010
@@ -650,6 +650,11 @@
         self.field_info = self._fieldinfo_class()
         # hardcoded for now
         self.parameters["InitialTime"] = 0.0
+        # These should be explicitly obtained from the file, but for now that
+        # will wait until a reorganization of the source tree and better
+        # generalization.
+        self.parameters["TopGridRank"] = 3
+        self.parameters["RefineBy"] = 2
         
     def _set_units(self):
         """