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Updated to marbl/miranda reader and adding support for miranda/samrai… #79

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Jun 10, 2024
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Updated to marbl/miranda reader and adding support for miranda/samrai… #79

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138 changes: 119 additions & 19 deletions pyranda/pyrandaMirandaReader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 )
Expand Down Expand Up @@ -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
Expand All @@ -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):
"""
Expand Down Expand Up @@ -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) )

Expand All @@ -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 = ""
Expand All @@ -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':
Expand All @@ -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]
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