def write2grid(prof, prof_name, grid_path, overwrite=False):
'''Write profile to a specified grid file.
Parameters:
prof -- 1D or 2D array, an equilibrium quantity to be
written to the grid file. An easy way to generate
an appropriate profile is to use the interpolate2grid(...)
routine above
prof_name -- str, name assigned to profile in grid file
grid_path -- str, path to the grid file to interpolate onto
overwrite -- bool, if False, this will prevent overwiting
a preexisting grid variable with the same name as prof_name
Returns:
True if the write is successful, False otherwise.
'''
grid_file = DataFile(grid_path, write=True)
if not overwrite and (prof_name in grid_file.list()):
raise ValueError(prof_name + ' is already in use in '
+ grid_path
+ '. Specify overwrite=True to overwrite existing profile')
grid_file.write(prof_name, prof)
return 0
def file_import(name):
f = DataFile(name) # Open file
varlist = f.list() # Get list of all variables in file
data = {} # Create empty dictionary
for v in varlist:
data[v] = f.read(v)
f.close()
return data
def file_import(name):
f = DataFile(name) # Open file
varlist = f.list() # Get list of all variables in file
data = {} # Create empty dictionary
for v in varlist:
data[v] = f.read(v)
f.close()
return data
def run(self):
# self.display.string += 'File' + '\n'
f = DataFile()
DataFile.open(f,self.path+self.filename)
varlist = f.list()
self.display.string += 'Variables in file :' + '\t' + 'No. of Dims.' + '\n'
for i in varlist:
self.display.string += str(i)+ '\t' + str(f.ndims(i))+ '\n'
f.close()
def split(nxpe, nype, path="data", output="./", informat="nc", outformat=None):
"""Split restart files across NXPE x NYPE processors.
Returns True on success
"""
if outformat == None:
outformat = informat
mxg = 2
myg = 2
npes = nxpe * nype
if npes <= 0:
print "ERROR: Negative or zero number of processors"
return False
if path == output:
print "ERROR: Can't overwrite restart files"
return False
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
if nfiles == 0:
print "ERROR: No restart files found"
return False
# Read old processor layout
f = DataFile(os.path.join(path, file_list[0]))
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print "ERROR: No data found"
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
if nfiles != old_npes:
print "WARNING: Number of restart files inconsistent with NPES"
print "Setting nfiles = " + str(old_npes)
nfiles = old_npes
if old_npes % old_nxpe != 0:
print "ERROR: Old NPES is not a multiple of old NXPE"
return False
old_nype = old_npes / old_nxpe
if nype % old_nype != 0:
print "SORRY: New nype must be a multiple of old nype"
return False
if nxpe % old_nxpe != 0:
print "SORRY: New nxpe must be a multiple of old nxpe"
return False
# Get dimension sizes
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
old_mysub = s[1] - 2*myg
mz = s[2]
break
f.close()
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print "Grid sizes: ", nx, ny, mz
# Create the new restart files
for mype in range(npes):
# Calculate X and Y processor numbers
pex = mype % nxpe
pey = int(mype / nxpe)
old_pex = int(pex / xs)
old_pey = int(pey / ys)
old_x = pex % xs
old_y = pey % ys
# Old restart file number
old_mype = old_nxpe * old_pey + old_pex
# Calculate indices in old restart file
xmin = old_x*mxsub
xmax = xmin + mxsub - 1 + 2*mxg
ymin = old_y*mysub
ymax = ymin + mysub - 1 + 2*myg
print "New: "+str(mype)+" ("+str(pex)+", "+str(pey)+")"
print " => "+str(old_mype)+" ("+str(old_pex)+", "+str(old_pey)+") : ("+str(old_x)+", "+str(old_y)+")"
def resizeY(newy, path="data", output=".", informat="nc", outformat=None,myg=2):
"""
Resize all the restart files in Y
"""
if outformat == None:
outformat = informat
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
if nfiles == 0:
print("ERROR: No restart files found")
return False
for i in range(nfiles):
# Open each data file
infname = os.path.join(path, "BOUT.restart."+str(i)+"."+informat)
outfname = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
print("Processing %s -> %s", infname, outfname)
infile = DataFile(infname)
outfile = DataFile(outfname, create=True)
# Copy basic information
for var in ["hist_hi", "NPES", "NXPE", "tt"]:
data = infile.read(var)
try:
# Convert to scalar if necessary
data = data[0]
except:
pass
outfile.write(var, data)
# Get a list of variables
varnames = infile.list()
for var in varnames:
if infile.ndims(var) == 3:
# Could be an evolving variable [x,y,z]
print(" -> " + var)
# Read variable from input
indata = infile.read(var)
nx,ny,nz = indata.shape
# y coordinate in input and output data
iny = (arange(ny) - myg + 0.5) / (ny - 2*myg)
outy = (arange(newy) - myg + 0.5) / (newy - 2*myg)
outdata = zeros([nx, newy, nz])
for x in range(nx):
for z in range(nz):
f = interp1d(iny, indata[x,:,z], bounds_error=False, fill_value=0.0)
outdata[x,:,z] = f(outy)
outfile.write(var, outdata)
infile.close()
outfile.close()
def redistribute(npes, path="data", nxpe=None, output=".", informat=None, outformat=None, mxg=2, myg=2):
"""Resize restart files across NPES processors.
Does not check if new processor arrangement is compatible with the branch cuts. In this respect restart.split is safer. However, BOUT++ checks the topology during initialisation anyway so this is not too serious.
Parameters
----------
npes : int
number of processors for the new restart files
path : string, optional
location of old restart files
nxpe : int, optional
number of processors to use in the x-direction (determines split: npes = nxpe * nype). Default is None which uses the same algorithm as BoutMesh (but without topology information) to determine a suitable value for nxpe.
output : string, optional
location to save new restart files
informat : string, optional
specify file format of old restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default uses the format of the first 'BOUT.restart.*' file listed by glob.glob.
outformat : string, optional
specify file format of new restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default is to use the same as informat.
Returns
-------
True on success
"""
if npes <= 0:
print("ERROR: Negative or zero number of processors")
return False
if path == output:
print("ERROR: Can't overwrite restart files")
return False
if informat == None:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*"))
else:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
# Read old processor layout
f = DataFile(file_list[0])
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print("ERROR: No data found")
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
old_nype = int(old_npes/old_nxpe)
if nfiles != old_npes:
print("WARNING: Number of restart files inconsistent with NPES")
print("Setting nfiles = " + str(old_npes))
nfiles = old_npes
if nfiles == 0:
print("ERROR: No restart files found")
return False
informat = file_list[0].split(".")[-1]
if outformat == None:
outformat = informat
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
if old_mxsub < 0:
if s[0] == 1:
old_mxsub = 1
mxg = 0
elif s[0] == 3:
old_mxsub = 1
mxg = 1
else:
print("Number of x points is wrong?")
return False
old_mysub = s[1] - 2*myg
if old_mysub < 0:
if s[1] == 1:
old_mysub = 1
myg = 0
elif s[1] == 3:
old_mysub = 1
myg = 1
else:
print("Number of y points is wrong?")
return False
mz = s[2]
break
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print("Grid sizes: ", nx, ny, mz)
if nxpe == None: # Copy algorithm from BoutMesh for selecting nxpe
ideal = sqrt(float(nx) * float(npes) / float(ny)) # Results in square domain
for i in range(1,npes+1):
if npes%i == 0 and nx%i == 0 and int(nx/i) >= mxg and ny%(npes/i) == 0:
# Found an acceptable value
# Warning: does not check branch cuts!
if nxpe==None or abs(ideal - i) < abs(ideal - nxpe):
nxpe = i # Keep value nearest to the ideal
if nxpe == None:
print("ERROR: could not find a valid value for nxpe")
return False
nype = int(npes/nxpe)
outfile_list = []
for i in range(npes):
outpath = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
outfile_list.append(DataFile(outpath, write=True, create=True))
infile_list = []
for i in range(old_npes):
inpath = os.path.join(path, "BOUT.restart."+str(i)+"."+outformat)
infile_list.append(DataFile(inpath))
old_mxsub = int(nx/old_nxpe)
old_mysub = int(ny/old_nype)
mxsub = int(nx/nxpe)
mysub = int(ny/nype)
for v in var_list:
ndims = f.ndims(v)
#collect data
if ndims == 0:
#scalar
data = f.read(v)
elif ndims == 2:
data = numpy.zeros( (nx+2*mxg,ny+2*nyg) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend]
elif ndims == 3:
data = numpy.zeros( (nx+2*mxg,ny+2*myg,mz) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend, :] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend, :]
else:
print("ERROR: variable found with unexpected number of dimensions,",ndims,v)
return False
# write data
for i in range(npes):
ix = i%nxpe
iy = int(i/nxpe)
outfile = outfile_list[i]
if v == "NPES":
outfile.write(v,npes)
elif v == "NXPE":
outfile.write(v,nxpe)
elif ndims == 0:
# scalar
outfile.write(v,data)
elif ndims == 2:
# Field2D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg])
elif ndims == 3:
# Field3D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg, :])
else:
print("ERROR: variable found with unexpected number of dimensions,",f.ndims(v))
f.close()
for infile in infile_list:
infile.close()
for outfile in outfile_list:
outfile.close()
return True
def create(averagelast=1, final=-1, path="data", output="./", informat="nc", outformat=None):
"""
Create restart files from data (dmp) files.
Inputs
======
averagelast Number of time points to average over.
Default is 1 i.e. just take last time-point
final The last time point to use. Default is last (-1)
path Path to the input data files
output Path where the output restart files should go
informat Format of the input data files
outformat Format of the output restart files
"""
if outformat == None:
outformat = informat
file_list = glob.glob(os.path.join(path, "BOUT.dmp.*."+informat))
nfiles = len(file_list)
print(("Number of data files: ", nfiles))
for i in range(nfiles):
# Open each data file
infname = os.path.join(path, "BOUT.dmp."+str(i)+"."+informat)
outfname = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
print((infname, " -> ", outfname))
infile = DataFile(infname)
outfile = DataFile(outfname, create=True)
# Get the data always needed in restart files
hist_hi = infile.read("iteration")
print(("hist_hi = ", hist_hi))
outfile.write("hist_hi", hist_hi)
t_array = infile.read("t_array")
tt = t_array[final]
print(("tt = ", tt))
outfile.write("tt", tt)
NXPE = infile.read("NXPE")
NYPE = infile.read("NYPE")
NPES = NXPE * NYPE
print(("NPES = ", NPES, " NXPE = ", NXPE))
outfile.write("NPES", NPES)
outfile.write("NXPE", NXPE)
# Get a list of variables
varnames = infile.list()
for var in varnames:
if infile.ndims(var) == 4:
# Could be an evolving variable
print((" -> ", var))
data = infile.read(var)
if averagelast == 1:
slice = data[final,:,:,:]
else:
slice = mean(data[(final - averagelast):final,:,:,:], axis=0)
print(slice.shape)
outfile.write(var, slice)
infile.close()
outfile.close()
def create(averagelast=1,
final=-1,
path="data",
output="./",
informat="nc",
outformat=None):
"""
Create restart files from data (dmp) files.
Inputs
======
averagelast Number of time points to average over.
Default is 1 i.e. just take last time-point
final The last time point to use. Default is last (-1)
path Path to the input data files
output Path where the output restart files should go
informat Format of the input data files
outformat Format of the output restart files
"""
if outformat == None:
outformat = informat
file_list = glob.glob(os.path.join(path, "BOUT.dmp.*." + informat))
nfiles = len(file_list)
print "Number of data files: ", nfiles
for i in range(nfiles):
# Open each data file
infname = os.path.join(path, "BOUT.dmp." + str(i) + "." + informat)
outfname = os.path.join(output,
"BOUT.restart." + str(i) + "." + outformat)
print infname, " -> ", outfname
infile = DataFile(infname)
outfile = DataFile(outfname, create=True)
# Get the data always needed in restart files
hist_hi = infile.read("iteration")
print "hist_hi = ", hist_hi
outfile.write("hist_hi", hist_hi)
t_array = infile.read("t_array")
tt = t_array[final]
print "tt = ", tt
outfile.write("tt", tt)
NXPE = infile.read("NXPE")
NYPE = infile.read("NYPE")
NPES = NXPE * NYPE
print "NPES = ", NPES, " NXPE = ", NXPE
outfile.write("NPES", NPES)
outfile.write("NXPE", NXPE)
# Get a list of variables
varnames = infile.list()
for var in varnames:
if infile.ndims(var) == 4:
# Could be an evolving variable
print " -> ", var
data = infile.read(var)
if averagelast == 1:
slice = data[final, :, :, :]
else:
slice = mean(data[(final - averagelast):final, :, :, :],
axis=0)
print slice.shape
outfile.write(var, slice)
infile.close()
outfile.close()
def resizeY(newy, path="data", output=".", informat="nc", outformat=None,myg=2):
"""
Resize all the restart files in Y
"""
if outformat == None:
outformat = informat
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
if nfiles == 0:
print("ERROR: No restart files found")
return False
for i in range(nfiles):
# Open each data file
infname = os.path.join(path, "BOUT.restart."+str(i)+"."+informat)
outfname = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
print("Processing %s -> %s", infname, outfname)
infile = DataFile(infname)
outfile = DataFile(outfname, create=True)
# Copy basic information
for var in ["hist_hi", "NPES", "NXPE", "tt"]:
data = infile.read(var)
try:
# Convert to scalar if necessary
data = data[0]
except:
pass
outfile.write(var, data)
# Get a list of variables
varnames = infile.list()
for var in varnames:
if infile.ndims(var) == 3:
# Could be an evolving variable [x,y,z]
print(" -> " + var)
# Read variable from input
indata = infile.read(var)
nx,ny,nz = indata.shape
# y coordinate in input and output data
iny = (arange(ny) - myg + 0.5) / (ny - 2*myg)
outy = (arange(newy) - myg + 0.5) / (newy - 2*myg)
outdata = zeros([nx, newy, nz])
for x in range(nx):
for z in range(nz):
f = interp1d(iny, indata[x,:,z], bounds_error=False, fill_value=0.0)
outdata[x,:,z] = f(outy)
outfile.write(var, outdata)
infile.close()
outfile.close()
def redistribute(npes, path="data", nxpe=None, output=".", informat=None, outformat=None, mxg=2, myg=2):
"""Resize restart files across NPES processors.
Does not check if new processor arrangement is compatible with the branch cuts. In this respect restart.split is safer. However, BOUT++ checks the topology during initialisation anyway so this is not too serious.
Parameters
----------
npes : int
number of processors for the new restart files
path : string, optional
location of old restart files
nxpe : int, optional
number of processors to use in the x-direction (determines split: npes = nxpe * nype). Default is None which uses the same algorithm as BoutMesh (but without topology information) to determine a suitable value for nxpe.
output : string, optional
location to save new restart files
informat : string, optional
specify file format of old restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default uses the format of the first 'BOUT.restart.*' file listed by glob.glob.
outformat : string, optional
specify file format of new restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default is to use the same as informat.
Returns
-------
True on success
"""
if npes <= 0:
print("ERROR: Negative or zero number of processors")
return False
if path == output:
print("ERROR: Can't overwrite restart files")
return False
if informat == None:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*"))
else:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
# Read old processor layout
f = DataFile(file_list[0])
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print("ERROR: No data found")
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
old_nype = int(old_npes/old_nxpe)
if nfiles != old_npes:
print("WARNING: Number of restart files inconsistent with NPES")
print("Setting nfiles = " + str(old_npes))
nfiles = old_npes
if nfiles == 0:
print("ERROR: No restart files found")
return False
informat = file_list[0].split(".")[-1]
if outformat == None:
outformat = informat
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
if old_mxsub < 0:
if s[0] == 1:
old_mxsub = 1
mxg = 0
elif s[0] == 3:
old_mxsub = 1
mxg = 1
else:
print("Number of x points is wrong?")
return False
old_mysub = s[1] - 2*myg
if old_mysub < 0:
if s[1] == 1:
old_mysub = 1
myg = 0
elif s[1] == 3:
old_mysub = 1
myg = 1
else:
print("Number of y points is wrong?")
return False
mz = s[2]
break
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print("Grid sizes: ", nx, ny, mz)
if nxpe == None: # Copy algorithm from BoutMesh for selecting nxpe
ideal = sqrt(float(nx) * float(npes) / float(ny)) # Results in square domain
for i in range(1,npes+1):
if npes%i == 0 and nx%i == 0 and int(nx/i) >= mxg and ny%(npes/i) == 0:
# Found an acceptable value
# Warning: does not check branch cuts!
if nxpe==None or abs(ideal - i) < abs(ideal - nxpe):
nxpe = i # Keep value nearest to the ideal
if nxpe == None:
print("ERROR: could not find a valid value for nxpe")
return False
nype = int(npes/nxpe)
outfile_list = []
for i in range(npes):
outpath = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
outfile_list.append(DataFile(outpath, write=True, create=True))
infile_list = []
for i in range(old_npes):
inpath = os.path.join(path, "BOUT.restart."+str(i)+"."+outformat)
infile_list.append(DataFile(inpath))
old_mxsub = int(nx/old_nxpe)
old_mysub = int(ny/old_nype)
mxsub = int(nx/nxpe)
mysub = int(ny/nype)
for v in var_list:
ndims = f.ndims(v)
#collect data
if ndims == 0:
#scalar
data = f.read(v)
elif ndims == 2:
data = numpy.zeros( (nx+2*mxg,ny+2*nyg) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend]
elif ndims == 3:
data = numpy.zeros( (nx+2*mxg,ny+2*myg,mz) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend, :] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend, :]
else:
print("ERROR: variable found with unexpected number of dimensions,",ndims,v)
return False
# write data
for i in range(npes):
ix = i%nxpe
iy = int(i/nxpe)
outfile = outfile_list[i]
if v == "NPES":
outfile.write(v,npes)
elif v == "NXPE":
outfile.write(v,nxpe)
elif ndims == 0:
# scalar
outfile.write(v,data)
elif ndims == 2:
# Field2D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg])
elif ndims == 3:
# Field3D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg, :])
else:
print("ERROR: variable found with unexpected number of dimensions,",f.ndims(v))
f.close()
for infile in infile_list:
infile.close()
for outfile in outfile_list:
outfile.close()
return True