def __init__(self, m3d):
# get 'grid_mask' variable from file
filepath = util.get_key(m3d, self, m3d.config, "Grid", str)
gridfile = util.get_hdf5_file(m3d, self, filepath)
grid = util.get_key(m3d, self, gridfile, "grid_mask",
Dataset) #gridfile["grid_mask"]
# masks
self.mask3d = mask3d = (grid[...] != grid.fillvalue)
self.mask2d = mask2d = mask3d[0, ...]
# not needed any more
gridfile.close()
# vector and profiles
self.nv = nv = mask3d.sum() # vector length
self.np = mask2d.sum() # profile count
self.npi = mask3d.sum(axis=0)[mask2d] # each profile length
# index permutation from nc/3d to tmm/1d
nc3d = mask3d[...].astype(">i4")
(nz, ny, nx) = nc3d.shape
nc3d[mask3d] = range(nv)
nc3d[mask3d] = nc3d[mask3d] + 1
nc1d = nc3d.reshape(nz, ny * nx).T.flat
self.nc2tmm = nc1d[nc1d != 0] - 1
# debug
util.debug(m3d, self, self, level=1)
def init_boundary_data(self, m3d):
self.b = []
self.nb = 0
self.nbi = []
config = self.config.get("Boundary data")
if config is None:
self.use_boundary = False
return
else:
self.use_boundary = True
self.boundary = boundary = util.get_key(
m3d, self, config, "Name, Count, Description, Unit, File", list)
self.boundary_path = util.get_key(m3d, self, config, "Path", str)
np = m3d.grid.np
nploc = m3d.load.nploc
self.nb = nb = len(boundary)
nbi = []
b = []
for i in range(nb):
count = boundary[i][1]
nbi.append(count)
bi = util.create_petsc_vectors(nbi[i], (nploc, np))
b.append(bi)
self.nbi = nbi
self.b = b
def init_domain_data(self, m3d):
self.d = []
self.nd = 0
self.ndi = []
config = self.config.get("Domain data")
if config is None:
self.use_domain = False
return
else:
self.use_domain = True
self.domain = domain = util.get_key(
m3d, self, config, "Name, Count, Description, Unit, File", list)
self.domain_path = util.get_key(m3d, self, config, "Path", str)
nv = m3d.grid.nv
nvloc = m3d.load.nvloc
self.nd = nd = len(domain)
ndi = []
d = []
for i in range(nd):
count = domain[i][1]
ndi.append(count)
di = util.create_petsc_vectors(ndi[i], (nvloc, nv))
d.append(di)
self.ndi = ndi
self.d = d
def __init__(self, m3d):
config = util.get_key(m3d, self, m3d.config, "Solver", dict)
self.type = util.get_key(m3d, self, config, "Type", str)
self.nl = util.get_key(m3d, self, config, "Count", int)
self.mon = util.get_key(m3d, self, config, "Monitor", bool)
self.yl = []
for y in m3d.tracer.y0:
self.yl.append(y.duplicate())
# debug
util.debug(m3d, self, self, level=1)
def __init__(self, m3d):
self.config = config = m3d.config.get("BGC")
if config is None:
self.use_bgc = False
else:
self.use_bgc = True
self.name = util.get_key(m3d, self, config, "Name", str)
# load bgc module
# must be placed in metos3d/bgc/<<name>>/<<sources>>
# must be compiled with: f2py -c <<sources>> -m <<name>>
# call to bgc routine must apply to:
# fortran: metos3dbgc(ny, nx, nu, nb, nd, dt, q, t, y, u, b, d)
# python: metos3dbgc(dt,q,t,y,u,b,d,[ny,nx,nu,nb,nd])
# module name: exchange '-' to '_'
modname = self.name.replace("-", "_")
self.mod = importlib.import_module("bgc." + self.name + "." +
modname)
self.init_parameter(m3d)
self.init_boundary_data(m3d)
self.init_domain_data(m3d)
# debug
util.debug(m3d, self, self, level=1)
def __init__(self, m3d):
config = util.get_key(m3d, self, m3d.config, "Time", dict)
self.t0 = util.get_key(m3d, self, config, "Start", float)
self.nt = util.get_key(m3d, self, config, "Count", int)
self.dt = util.get_key(m3d, self, config, "Step", float)
tracer = m3d.tracer
ny = tracer.ny
y0 = tracer.y0
bgc = m3d.bgc
b = bgc.b
nb = bgc.nb
nbi = bgc.nbi
bj = []
for bi in b:
bj.append(bi[0].duplicate())
self.bj = bj
d = bgc.d
nd = bgc.nd
ndi = bgc.ndi
dj = []
for di in d:
dj.append(di[0].duplicate())
self.dj = dj
yj = []
yexpj = []
qj = []
for yi in y0:
yj.append(yi.duplicate())
yexpj.append(yi.duplicate())
qi = yi.duplicate()
qi.zeroEntries()
qi.assemble()
qj.append(qi)
self.yj = yj
self.yexpj = yexpj
self.qj = qj
# debug
util.debug(m3d, self, self, level=1)
def __init__(self, m3d):
config = util.get_key(m3d, self, m3d.config, "Tracer", dict)
self.tracer = tracer = util.get_key(m3d, self, config,
"Name, Value, Unit, Description",
list)
self.output = config.get("Output")
self.input = config.get("Input")
# global and local vector length
nv = m3d.grid.nv
nvloc = m3d.load.nvloc
self.ny = ny = len(tracer)
self.y0 = util.create_petsc_vectors(ny, (nvloc, nv))
# debug
util.debug(m3d, self, self, level=1)
def __init__(self, m3d):
self.config = config = m3d.config.get("TMM")
if config is None:
self.use_tmm = False
else:
self.use_tmm = True
self.path = util.get_key(m3d, self, config, "Path", str)
self.init_explicit(m3d)
self.init_implicit(m3d)
# debug
util.debug(m3d, self, self, level=1)
def init_parameter(self, m3d):
self.u = numpy.array([], dtype="f8") # f2py, no copy as such
self.nu = 0
config = self.config.get("Parameter")
if config is None:
self.use_param = False
return
else:
self.use_param = True
self.parameter = parameter = util.get_key(
m3d, self, config, "Name, Value, Unit, Description", list)
self.nu = nu = len(parameter)
u = []
for i in range(nu):
value = parameter[i][1]
u.append(value)
self.u = numpy.array(u)
def __init__(self, argv):
"""
check computation model ...
print version,
print number of processes,
attributes ...
creates instances ...
initialize metos3d context,
Parameters:
argv: list with command arguments, file path of yaml conf file
"""
# version and runtime context
self.version = version = VERSION
self.comm = comm = PETSc.COMM_WORLD
self.size = size = comm.size
self.rank = rank = comm.rank
# config
self.config = util.get_config_from_yaml_file(self, argv)
# debug level
self.debug = util.get_key(self, self, self.config, "Debug", int)
util.debug(self, self, "--- init " + 100 * "-", level=1)
util.debug(self, self, self, level=1)
# init
self.grid = Grid(self)
self.load = Load(self)
self.tracer = Tracer(self)
self.bgc = BGC(self)
self.tmm = TMM(self)
self.time = Time(self)
self.solver = Solver(self)