Updated to marbl/miranda reader and adding support for miranda/samrai files.

Author: flow-phys

pyranda/pyrandaMirandaReader.py

@@ -70,28 +70,46 @@ def __init__(self, rootdir, var_list, periodic=[False,False,False]):
         # Read in domain meta-data from master proc
         proc_num = 0
         filename = join(self.data_dir,'marbl_' + str(cycle).zfill(7) + '_' + str(proc_num).zfill(7) + '.hdf5')
-        header = 'datagroup_' + str(proc_num).zfill(7)
+        header = 'datagroup' #+ str(proc_num).zfill(7)
 
         # Load hdf5 file
         f = h5py.File(filename,'r')
 
         # Processor arrangement
-        px = int(f[header + path_proc + 'px/value'].value)
-        py = int(f[header + path_proc + 'py/value'].value)
-        pz = int(f[header + path_proc + 'pz/value'].value)
-        self.procs = [px,py,pz]
+        px = int(f[header + path_proc + 'px/value'][0])
+        py = int(f[header + path_proc + 'py/value'][0])
+        pz = int(f[header + path_proc + 'pz/value'][0])
 
         # Grid spacing
-        dx = f[header + path_grid + 'dx/value'].value
-        dy = f[header + path_grid + 'dy/value'].value
-        dz = f[header + path_grid + 'dz/value'].value
-
-        # Import data as numpy array
-        # Grab grid size for verificiation  - Static location in blueprint?
-        self.ax = ax = int(f[header + path_coord + 'i/value'].value) - 1
-        self.ay = ay = int(f[header + path_coord + 'j/value'].value) - 1
-        self.az = az = int(f[header + path_coord + 'k/value'].value) - 1
+        try:
+            dx = f[header + path_grid + 'dx/value'][0]
+            self.ax = ax = int(f[header + path_coord + 'i/value'][0]) - 1
+        except:
+            dx = 1.0
+            ax = 1
+
+        try:
+            dy = f[header + path_grid + 'dy/value'][0]
+            self.ay = ay = int(f[header + path_coord + 'j/value'][0]) - 1
+        except:
+            dy = 1.0
+            ay = 1
+
+        try:
+            dz = f[header + path_grid + 'dz/value'][0]
+            self.az = az = int(f[header + path_coord + 'k/value'][0]) - 1
+        except:
+            dz = 1.0
+            az = 1
+
+        # Correction for x-z 2D domains
+        if (ax > 1) and (ay > 1) and (pz > 1) and (py==1):
+            py = pz
+            pz = 1
 
+        self.procs = [px,py,pz]
+            
+        
         # Need to get a mesh object here
         x1,xn = 0, dx*ax*px
         y1,yn = 0, dy*ay*py
@@ -102,6 +120,7 @@ def __init__(self, rootdir, var_list, periodic=[False,False,False]):
         mesh_options['xn'] = [xn,yn,zn]
         mesh_options['nn'] = [nx,ny,nz]
         mesh_options['periodic'] = periodic
+
 
         # Make pyranda instance
         self.pysim = pyrandaSim( rootdir + '_pyranda', mesh_options )
@@ -141,6 +160,8 @@ def update(self, cycle,fileType=0):
             self.data_dir = join(self.rootdir,'marbl_' + str(cycle).zfill(7))
         elif fileType == 1: # native miranda vis files
             self.data_dir = join(self.rootdir,'vis' + str(cycle).zfill(7))
+        elif fileType == 2: # native miranda vis files
+            self.data_dir = join(self.rootdir,'visit_dump.' + str(cycle).zfill(5))
 
 
         # Check if file exists
@@ -166,6 +187,22 @@ def setNativeVizDict(self,rosetta):
         for ii in self.var_list:
             varDict[ii] = miranda_viz_names[ rosetta[ii] ]
         self.var_index_dict = varDict
+
+
+    def getMirandaSamraiVariables(self):
+
+        # Read in the first vis file to get variable list
+        data_dir = join(self.rootdir,'visit_dump.' + str(0).zfill(5))
+        filename = join(data_dir, 'processor_cluster.' + str(0).zfill(5) + ".samrai" )
+
+        # Load hdf5 file
+        data = h5py.File(filename,'r')
+
+        # Use the 0-proc for variables
+        sproc = str(0).zfill(5)
+        header = 'processor.' + sproc + "/level.00000/patch." + sproc + "/"
+        visit_vars = [dd for dd in data[header].keys()]
+        return visit_vars
 
 def readChunkMiranda(pysim,procs,procMap,dump,cycle,var_list,var_index_dict,fileType=0):
     """
@@ -250,6 +287,7 @@ def readChunkMiranda(pysim,procs,procMap,dump,cycle,var_list,var_index_dict,file
                                                               Lj1:Ljf,
                                                               Lk1:Lkf]
 
+                    
             elif fileType == 1: # Miranda native graphics files
                 filename = join(dump, 'p' + str(proc_num).zfill(8) )
 
@@ -274,7 +312,25 @@ def readChunkMiranda(pysim,procs,procMap,dump,cycle,var_list,var_index_dict,file
                                               Kk1:Kkf] = DATA[Li1:Lif,
                                                               Lj1:Ljf,
                                                               Lk1:Lkf]
-                    
+
+
+            elif fileType == 2: # Samrai, single level only data
+                filename = join(dump, 'processor_cluster.' + str(proc_num).zfill(5) + ".samrai" )
+
+                # Load hdf5 file
+                f = h5py.File(filename,'r')
+                file_grid_shape = ( int(ax), int(ay), int(az) )
+                
+                for var in var_list:
+                    DATA = import_field_samrai(f,iproc,var,file_grid_shape)    
+                    pysim.variables[var].data[Ki1:Kif,
+                                              Kj1:Kjf,
+                                              Kk1:Kkf] = DATA[Li1:Lif,
+                                                              Lj1:Ljf,
+                                                              Lk1:Lkf]
+
+
+    
 
 def convert(str_array):     # Convert numpy array of binary encoded chars to string
     s = ""
@@ -284,10 +340,21 @@ def convert(str_array):     # Convert numpy array of binary encoded chars to str
 
 def import_field(data, proc_num, var):
 
-    header = 'datagroup_' + str(proc_num).zfill(7)
-    nx = int(data[header + path_coord + 'i/value'].value) - 1
-    ny = int(data[header + path_coord + 'j/value'].value) - 1
-    nz = int(data[header + path_coord + 'k/value'].value) - 1
+    header = 'datagroup' #+ str(proc_num).zfill(7)
+    try:
+        nx = int(data[header + path_coord + 'i/value'][0]) - 1
+    except:
+        nx = 1
+    try:
+        ny = int(data[header + path_coord + 'j/value'][0]) - 1
+    except:
+        ny = 1
+    try:
+        nz = int(data[header + path_coord + 'k/value'][0]) - 1
+    except:
+        nz = 1
+
+        
     n = (nx,ny,nz)
 
     if var[0] == 'Y':
@@ -303,3 +370,36 @@ def import_field(data, proc_num, var):
         #print('Finished importing ' + var + '!')
 
     return numpy.reshape(arr,n,order='F')  
+
+def import_field_samrai(data, proc_num, var, n):
+
+    sproc = str(proc_num).zfill(5)
+    header = 'processor.' + sproc + "/level.00000/patch." + sproc + "/"
+        
+    tmp = data[header + var]       # Temp data holder
+    arr = numpy.zeros(tmp.shape,dtype='float64')    # Initialize array using dataset shape
+    tmp.read_direct(arr)       # Directly read in hdf5 dataset to numpy array
+
+    ax = n[0]
+    ay = n[1]
+    az = n[2]
+
+    xslc = slice(0,None)
+    yslc = slice(0,None)
+    zslc = slice(0,None)
+    
+    if ax > 1:
+        ax +=2
+        xslc = slice(1,-1)
+    if ay > 1:
+        ay +=2
+        yslc = slice(1,-1)
+    if az > 1:
+        az +=2
+        zslc = slice(1,-1)
+    
+    n_buffer = (ax,ay,az)
+    
+    amrdata = numpy.reshape(arr,n_buffer,order='F')
+    
+    return amrdata[xslc,yslc,zslc]