[cig-commits] r20139 - short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d

[brad at geodynamics.org]

Author: brad
Date: 2012-05-15 15:14:32 -0700 (Tue, 15 May 2012)
New Revision: 20139

Modified:
   short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_offfaultdata.py
   short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_onfaultdata.py
Log:
Switched from tables to h5py.

Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_offfaultdata.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_offfaultdata.py	2012-05-15 22:11:15 UTC (rev 20138)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_offfaultdata.py	2012-05-15 22:14:32 UTC (rev 20139)
@@ -19,7 +19,7 @@
 outputRoot = "scecfiles/%s_%s_%03dm_gradient" % (sim, cell,dx)
 
 # ----------------------------------------------------------------------
-import tables
+import h5py
 import numpy
 import time
 
@@ -38,8 +38,8 @@
 targets[:,1] += 2000.0
 
 
-h5 = tables.openFile("%s.h5" % (inputRoot), 'r')
-vertices = h5.root.geometry.vertices[:]
+h5 = h5py.File("%s.h5" % (inputRoot), 'r', driver="sec2")
+vertices = h5['geometry/vertices'][:]
 ntargets = targets.shape[0]
 indices = []
 tolerance = 1.0e-6
@@ -53,21 +53,17 @@
 print "Coordinates of selected points:\n",vertices[indices,:]
 
 # Get datasets
-disp = h5.root.vertex_fields.displacement[:]
-vel = h5.root.vertex_fields.velocity[:]
+disp = h5['vertex_fields/displacement'][:]
+vel = h5['vertex_fields/velocity'][:]
+timeStamps =  h5['time'][:]
 
-# BEGIN TEMPORARY
-#timeStamps =  h5.root.vertex_fields.time (not yet available)
-ntimesteps = disp.shape[0]
-timeStamps = numpy.linspace(0, dt*ntimesteps, ntimesteps, endpoint=True)
-# END TEMPORARY
+h5.close()
 
+
 disp = disp[:,indices,:]
 vel = vel[:,indices,:]
 zero = numpy.zeros( (ntimesteps, 1), dtype=numpy.float64)
 
-h5.close()
-
 # Write data
 headerA = \
     "# problem = %s-2D\n" % sim.upper() + \

Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_onfaultdata.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_onfaultdata.py	2012-05-15 22:11:15 UTC (rev 20138)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv14-2d/tabulate_onfaultdata.py	2012-05-15 22:14:32 UTC (rev 20139)
@@ -19,7 +19,7 @@
 outputRoot = "scecfiles/%s_%s_%03dm_gradient" % (sim, cell,dx)
 
 # ----------------------------------------------------------------------
-import tables
+import h5py
 import numpy
 import time
 
@@ -27,8 +27,8 @@
 def extract(fault, targets):
     tolerance = 1.0e-6
 
-    h5 = tables.openFile("%s-%s.h5" % (inputRoot, fault), 'r')
-    vertices = h5.root.geometry.vertices[:]
+    h5 = h5py.File("%s-%s.h5" % (inputRoot, fault), 'r', driver="sec2")
+    vertices = h5['geometry/vertices'][:]
     ntargets = targets.shape[0]
     indices = []
     for target in targets:
@@ -41,22 +41,18 @@
     print "Coordinates of selected points:\n",vertices[indices,:]
 
     # Get datasets
-    slip = h5.root.vertex_fields.slip[:]
-    slip_rate = h5.root.vertex_fields.slip_rate[:]
-    traction = h5.root.vertex_fields.traction[:]
+    slip = h5['vertex_fields/slip'][:]
+    slip_rate = h5['vertex_fields/slip_rate'][:]
+    traction = h5['vertex_fields/traction'][:]
 
-    # BEGIN TEMPORARY
-    #timeStamps =  h5.root.vertex_fields.time (not yet available)
-    ntimesteps = slip.shape[0]
-    timeStamps = numpy.linspace(dt, dt*ntimesteps, ntimesteps-1, endpoint=True)
-    # END TEMPORARY
+    timeStamps =  h5['time'][:]
 
+    h5.close()
+
     slip = slip[1:,indices,:]
     slip_rate = slip_rate[1:,indices,:]
     traction = traction[1:,indices,:]
 
-    h5.close()
-
     headerA = \
         "# problem = %s-2D\n" % sim.upper() + \
         "# author = Brad Aagaard\n" + \