def get_sets(self):
nodes=Grid(self.parameters["NP"])
if self.coordinates=="cartesian":
nodes.x=self.p[:,0] | units.m
nodes.y=self.p[:,1] | units.m
else:
nodes.lon=self.p[:,0] | units.deg
nodes.lat=self.p[:,1] | units.deg
nodes.depth=self.p[:,2] | units.m
elements=Grid(self.parameters["NE"])
elements.nodes=[(x[1]-1,x[2]-1,x[3]-1) for x in self.t]
elev_boundary=[]
for type_,seg in self.elev_spec_boundary_seg:
indices=seg-1
b=Grid(len(indices))
b.nodes=indices
b.type=type_
elev_boundary.append(b)
flow_boundary=[]
for type_,seg in self.flow_spec_boundary_seg:
indices=seg-1
b=Grid(len(indices))
b.nodes=indices
b.type=type_
flow_boundary.append(b)
return nodes,elements,elev_boundary,flow_boundary
def test54(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test23" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
stars[0].gas = gas[0][0]
stars[1].gas = gas[1][0]
self.assertAlmostRelativeEquals(stars[0].gas.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(stars[1].gas.y, 4.0 | units.km)
io.write_set_to_file(stars,
output_file,
"hdf5",
version=self.store_version())
loaded_stars = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
self.assertAlmostRelativeEquals(loaded_stars[0].gas.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_stars[1].gas.y, 4.0 | units.km)
def test27(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test27" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10,
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p)
loaded_grid = instance.load_grid()
self.assertEqual(loaded_grid.shape, shape)
loaded_mass_in_kg = loaded_grid.mass.value_in(units.kg)
previous_mass_in_kg = p.mass.value_in(units.kg)
for expected, actual in zip(previous_mass_in_kg, loaded_mass_in_kg):
self.assertEqual(expected, actual)
instance.close()
def test20(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test20" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = (numpy.asarray([x * 2.0
for x in range(p.size)])).reshape(shape)
io.write_set_to_file(p,
output_file,
"hdf5",
version=self.store_version())
loaded = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
loaded = self.get_version_in_store(loaded)
self.assertAlmostRelativeEquals(p.mass[0][1][2], 24)
self.assertAlmostRelativeEquals(p[0][1][2].mass, 24)
def test12(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test12" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
io.write_set_to_file(p.savepoint(timestamp=2 | units.Myr,
scale=1 | units.kg),
output_file,
"hdf5",
version=self.store_version())
loaded_particles = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
loaded_particles = self.get_version_in_store(loaded_particles)
a = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(a.timestamp, 2 | units.Myr)
self.assertAlmostRelativeEquals(a.scale, 1 | units.kg)
def test6(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(
test_results_path, "test6_grid" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p.savepoint(1 | units.Myr))
loaded_grid = self.get_version_in_store(instance.load_grid())
self.assertAlmostRelativeEquals(loaded_grid.get_timestamp(),
1 | units.Myr)
self.assertEqual(loaded_grid.shape, shape)
self.assertEqual(loaded_grid[0][0][0].mass, 0 | units.kg)
self.assertAlmostRelativeEquals(loaded_grid[..., 1, 1].mass, p[..., 1,
1].mass)
instance.close()
def load(self):
dataset = Dataset(self.filename)
shape = ()
order = dict()
for i, (key, d) in enumerate(dataset.dimensions.items()):
shape += (len(d), )
order[key] = i
grid = Grid(*shape[0:2])
for s in dataset.ncattrs():
setattr(grid.collection_attributes, s, getattr(dataset, s))
for name, var in dataset.variables.items():
perm = [order[x] for x in var.dimensions]
if hasattr(var, "units"):
unit = units_lookup[var.units]
else:
unit = units.none
setattr(grid, name, numpy.array(var).transpose(tuple(perm)) | unit)
self.dataset = dataset
return grid
def __init__(self, filename, nx, ny):
self.filename = filename
import os.path
import sys
if not os.path.isfile(filename):
sys.exit("Error: No such file " + filename)
raw = numpy.fromfile(filename).newbyteorder('S')
grid = raw.reshape((7, ny, nx))
# lats=grid[0,:,:]/numpy.pi*180
# lons=grid[1,:,:]/numpy.pi*180
self.lat = lats = grid[0, :, :]
self.lon = lons = grid[1, :, :]
self.htn = htn = grid[2, :, :]
self.hte = hte = grid[3, :, :]
self.hus = hus = grid[4, :, :]
self.huw = huw = grid[5, :, :]
self.angle = angle = grid[6, :, :]
#nodes is the U-grid
self.nodes = nodes = Grid(ny * nx)
nodes.lats = lats | units.rad
nodes.lons = lons | units.rad
def get_sets(self):
nodes = Grid(self.parameters["NP"])
if self.coordinates == "cartesian":
nodes.x = self.p[:, 0] | units.m
nodes.y = self.p[:, 1] | units.m
else:
nodes.lon = self.p[:, 0] | units.deg
nodes.lat = self.p[:, 1] | units.deg
nodes.vmark = self.vmark
elements = Grid(self.parameters["NE"])
elements.n1 = [(x[0]) for x in self.t]
elements.n2 = [(x[1]) for x in self.t]
elements.n3 = [(x[2]) for x in self.t]
return nodes, elements #,elev_boundary,flow_boundary
def test26(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test26"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
p = Grid(20)
io.write_set_to_file(p, output_file, format='amuse', version = self.store_version())
os.remove(output_file)
def test54b(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test24" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
gas[0][0].particle = stars[0]
gas[1][2].particle = stars[0]
gas[1][0].particle = stars[1]
#stars[0].gas = gas[0][0]
#stars[1].gas = gas[1][0]
self.assertAlmostRelativeEquals(gas[0][0].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][2].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][0].particle.x, 2.0 | units.km)
io.write_set_to_file(gas,
output_file,
"hdf5",
version=self.store_version())
loaded_gas = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][2].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][0].particle.x,
2.0 | units.km)
self.assertEqual(id(loaded_gas[0][0].particle.get_containing_set()),
id(loaded_gas[1][2].particle.get_containing_set()))
self.assertEqual(loaded_gas.particle.shape, loaded_gas.shape)
gas_copy = loaded_gas.copy()
gas_copy[0][0].particle.x = 3 | units.km
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[0][0].particle.x,
3.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[1][2].particle.x,
3.0 | units.km)
def test29(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test29"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
particles = Grid(10)
particles.attribute1 = "normal"
particles.attribute2 = u"unicode"
io.write_set_to_file(particles,output_file, format='amuse', version = self.store_version())
output = io.read_set_from_file(output_file, format='amuse')
self.assertEquals(output[0].attribute2, u"unicode")
def test59(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test59"+self.store_version()+".h5")
if os.path.exists(output_file):
os.remove(output_file)
g=Grid(10,10)
p=Particles(2)
p[0].sub=g[0:5]
io.write_set_to_file(p, output_file,"amuse", version=self.store_version())
z = io.read_set_from_file(output_file,"amuse")
os.remove(output_file)
def generate_grid(self,n=10,m=10, FI0=-80. | units.deg, FI1=80. | units.deg,
L0=0. | units.deg, L1=360. | units.deg,
dFI=None, dL=None):
if dFI is None:
dFI=(FI1-FI0)/n
if dL is None:
dL=(L1-L0)/m
FI,L=numpy.mgrid[in_deg(FI0):in_deg(FI1):in_deg(dFI),
in_deg(L0):in_deg(L1):in_deg(dL)]
FI=FI|units.deg
L=L|units.deg
n,m=FI.shape
fi,l=self.forward_transform(FI,L)
grid=Grid((n,m))
grid.FI=FI
grid.L=L
grid.lat=to_deg(fi)
grid.lon=to_deg(l)
return grid
def test56(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test26" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
number_of_particles = 10
p = Particles(number_of_particles)
p.mass = [x * 2.0 for x in range(number_of_particles)] | units.kg
p.model_time = 2.0 | units.s
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
io.write_set_to_file(p,
output_file,
"hdf5",
particle=p[1],
particles=p,
gridpoint=gas[0][0],
grid=gas,
version=self.store_version())
loaded_particles = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version(),
copy_history=False,
close_file=False)
attributes = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(attributes.particle.mass,
loaded_particles[1].mass)
self.assertEquals(attributes.particle.key, loaded_particles[1].key)
self.assertEquals(id(attributes.particles), id(loaded_particles))
self.assertAlmostRelativeEquals(attributes.gridpoint.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(attributes.grid[0][0].y,
1.0 | units.km)
def derive_stellar_structure(self):
sorted = self.sph_particles.pressure.argsort()[::-1]
binned = sorted.reshape((-1, self.particles_per_zone))
stellar_model = Grid(binned.shape[0])
stellar_model.dmass = self.sph_particles.mass[binned].sum(axis=1)
stellar_model.mass = stellar_model.dmass.accumulate()
stellar_model.pressure = self.sph_particles.pressure[binned].sum(
axis=1)
stellar_model.rho = stellar_model.dmass / (
self.sph_particles.mass /
self.sph_particles.density)[binned].sum(axis=1)
stellar_model.radius = (
(3 / (4 * numpy.pi)) * stellar_model.dmass /
stellar_model.rho).accumulate()**(1.0 / 3.0) * 1
stellar_model.temperature = (
(self.sph_particles.mass * self.sph_particles.u *
self.sph_particles.mu)[binned].sum(axis=1) /
(1.5 * constants.kB * stellar_model.dmass)).as_quantity_in(units.K)
zeros = numpy.zeros(len(stellar_model.dmass))
stellar_model.luminosity = zeros - 1 | units.LSun
attribute_names = self.sph_particles.get_attribute_names_defined_in_store(
)
for attribute, name in [("h1", "X_H"), ("he4", "X_He"), ("c12", "X_C"),
("n14", "X_N"), ("o16", "X_O"),
("ne20", "X_Ne"), ("mg24", "X_Mg"),
("si28", "X_Si"), ("fe56", "X_Fe")]:
if attribute in attribute_names:
setattr(
stellar_model, name, (self.sph_particles.mass * getattr(
self.sph_particles, attribute))[binned].sum(axis=1) /
stellar_model.dmass)
else:
setattr(stellar_model, name, zeros)
return stellar_model
