def test_can_run_with_hex():
"""Test that model can run with hex model grid."""
# Set up a 5x5 grid with open boundaries and low initial elevations.
mg = HexModelGrid(7, 7)
z = mg.add_zeros("node", "topographic__elevation")
z[:] = 0.01 * mg.x_of_node
# Create a D8 flow handler
fa = FlowAccumulator(mg, flow_director="FlowDirectorSteepest")
# Parameter values for test 1
U = 0.001
dt = 10.0
# Create the Space component...
sp = Space(
mg,
K_sed=0.00001,
K_br=0.00000000001,
F_f=0.5,
phi=0.1,
H_star=1.,
v_s=0.001,
m_sp=0.5,
n_sp=1.0,
sp_crit_sed=0,
sp_crit_br=0,
)
# ... and run it to steady state.
for i in range(2000):
fa.run_one_step()
sp.run_one_step(dt=dt)
z[mg.core_nodes] += U * dt
def test_non_raster():
"""Test a hex model grid."""
grid = HexModelGrid(7, 3, dx=10)
_ = grid.add_zeros('node', 'topographic__elevation')
param_dict = {'faulted_surface': 'topographic__elevation',
'fault_dip_angle': 90.0,
'fault_throw_rate_through_time': {'time': [0, 9, 10],
'rate': [0, 0, 0.05]},
'fault_trace': {'y1': 30.0,
'x1': 30.0,
'y2': 20.0,
'x2': 0.0},
'include_boundaries': True}
nf = NormalFault(grid, **param_dict)
# plotting, to test this. it works!
#import matplotlib.pyplot as plt
#plt.figure()
#imshow_grid(grid, nf.faulted_nodes, color_for_background='y')
#plt.plot(grid.x_of_node, grid.y_of_node, 'c.')
#plt.plot([param_dict['fault_trace']['x1'], param_dict['fault_trace']['x2']],
# [param_dict['fault_trace']['y1'], param_dict['fault_trace']['y2']], 'r')
#plt.show()
out = np.array([ True, True, True, True, True, True, True, False, True,
True, True, True, False, False, False, False, True, True,
False, False, False, False, False, False, False, False, False,
False, False, False], dtype=bool)
assert_array_equal(nf.faulted_nodes, out)
def test_functions_with_Hex():
mg = HexModelGrid(10, 10)
z = mg.add_zeros("node", "topographic__elevation")
z += mg.x_of_node + mg.y_of_node
fa = FlowAccumulator(mg)
fa.run_one_step()
ch = ChiFinder(mg, min_drainage_area=1.0, reference_concavity=1.0)
ch.calculate_chi()
def test_flow__distance_irregular_grid_d4():
"""Test to demonstrate that flow__distance utility works as expected with irregular grids"""
# instantiate a model grid
dx = 1.0
hmg = HexModelGrid(5, 3, dx)
# instantiate and add the elevation field
hmg.add_field(
"topographic__elevation", hmg.node_x + np.round(hmg.node_y), at="node"
)
# instantiate the expected flow__distance array
flow__distance_expected = np.array(
[
0.0,
0.0,
0.0,
0.0,
0.0,
dx,
0.0,
0.0,
dx,
dx,
2.0 * dx,
0.0,
0.0,
2.0 * dx,
2.0 * dx,
0.0,
0.0,
0.0,
0.0,
]
)
# setting boundary conditions
hmg.set_closed_nodes(hmg.boundary_nodes)
# calculating flow directions with FlowAccumulator component: D4 algorithm
fr = FlowAccumulator(hmg, flow_director="D4")
fr.run_one_step()
# calculating flow distance map
flow__distance = calculate_flow__distance(hmg, add_to_grid=True, noclobber=False)
# test that the flow__distance utility works as expected
assert_almost_equal(flow__distance_expected, flow__distance, decimal=10)
def test_save_and_load_hex():
"""Test saving and loading of a HexModelGrid."""
mg1 = HexModelGrid(3, 3, 1.0)
mg1.add_zeros("node", "topographic__elevation")
save_grid(mg1, "testsavedgrid.grid")
mg2 = load_grid("testsavedgrid.grid")
assert mg1.x_of_node[0] == mg2.x_of_node[0]
assert_array_equal(mg1.status_at_node, mg2.status_at_node)
for name in mg1.at_node:
assert_array_equal(mg1.at_node[name], mg2.at_node[name])
def test_transitions_as_ids():
"""Test passing from-state and to-state IDs instead of tuples """
mg = HexModelGrid(3, 2, 1.0, orientation="vertical", reorient_links=True)
nsd = {0: "zero", 1: "one"}
xnlist = []
xnlist.append(Transition(2, 3, 1.0, "transitioning"))
nsg = mg.add_zeros("node", "node_state_grid")
cts = HexCTS(mg, nsd, xnlist, nsg)
assert cts.num_link_states == 4, "wrong number of transitions"
def test_oriented_hex_cts():
"""Tests instantiation of an OrientedHexCTS() object"""
mg = HexModelGrid(3, 2, 1.0, orientation="vertical", reorient_links=True)
nsd = {0: "zero", 1: "one"}
xnlist = []
xnlist.append(Transition((0, 1, 0), (1, 1, 0), 1.0, "transitioning"))
nsg = mg.add_zeros("node", "node_state_grid")
ohcts = OrientedHexCTS(mg, nsd, xnlist, nsg)
assert_equal(ohcts.num_link_states, 12)
assert_array_equal(ohcts.link_orientation, [2, 1, 0, 0, 0, 2, 1, 0, 2, 1, 0])
def test_hex_cts():
"""Tests instantiation of a HexCTS() object"""
mg = HexModelGrid(3, 2, 1.0, orientation='vertical', reorient_links=True)
nsd = {0 : 'zero', 1 : 'one'}
xnlist = []
xnlist.append(Transition((0,1,0), (1,1,0), 1.0, 'transitioning'))
nsg = mg.add_zeros('node', 'node_state_grid')
hcts = HexCTS(mg, nsd, xnlist, nsg)
assert_equal(hcts.num_link_states, 4)
assert_array_equal(hcts.link_orientation, [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_grid_type_testing():
"""Test that only the right grids can be implemented."""
dx=(2./(3.**0.5))**0.5
hmg = HexModelGrid(9,5, dx)
z = hmg.add_field('topographic__elevation', hmg.node_x + np.round(hmg.node_y), at = 'node')
# D8 is ONLY RASTER
with pytest.raises(NotImplementedError):
FlowDirectorD8(hmg)
# DINF IS ONLY RASTER RASTER
with pytest.raises(NotImplementedError):
FlowDirectorDINF(hmg)
def test_handle_grid_mismatch():
"""Test error handling when user passes wrong grid type."""
mg = HexModelGrid(3, 2, 1.0, orientation="vertical", reorient_links=True)
nsd = {0: "zero", 1: "one"}
xnlist = []
xnlist.append(Transition(2, 3, 1.0, "transitioning"))
nsg = mg.add_zeros("node", "node_state_grid")
assert_raises(TypeError, RasterCTS, mg, nsd, xnlist, nsg)
assert_raises(TypeError, OrientedRasterCTS, mg, nsd, xnlist, nsg)
mg = RasterModelGrid((3, 3))
assert_raises(TypeError, HexCTS, mg, nsd, xnlist, nsg)
assert_raises(TypeError, OrientedHexCTS, mg, nsd, xnlist, nsg)
def test_neighbor_shaping_hex():
hmg = HexModelGrid(6, 5, dx=1.)
hmg.add_zeros("node", "topographic__elevation", dtype=float)
hmg.add_zeros("node", "topographic__steepest_slope", dtype=float)
hmg.add_zeros("node", "flow__receiver_node", dtype=int)
hmg.add_zeros("node", "flow__link_to_receiver_node", dtype=int)
lmb = LakeMapperBarnes(hmg, redirect_flow_steepest_descent=True)
for arr in (lmb._neighbor_arrays, lmb._link_arrays):
assert len(arr) == 1
assert arr[0].shape == (hmg.number_of_nodes, 6)
assert len(lmb._neighbor_lengths) == hmg.number_of_links
def __init__(self, grid=None, node_state=None, propid=None, prop_data=None, prop_reset_value=None):
# If needed, create grid
if grid is None:
num_rows = _DEFAULT_NUM_ROWS
num_cols = _DEFAULT_NUM_COLS
self.grid = HexModelGrid(num_rows, num_cols, dx=1.0,
orientation='vertical',
shape='rect', reorient_links=True)
else:
# Make sure caller passed the right type of grid
assert (grid.orientation=='vertical'), \
'Grid must have vertical orientation'
# Keep a reference to the grid
self.grid = grid
# If needed, create node-state grid
if node_state is None:
self.node_state = self.grid.add_zeros('node', 'node_state_map')
else:
#print 'setting node state'
self.node_state = node_state
# Remember the # of rows and cols
self.nr = self.grid.number_of_node_rows
self.nc = self.grid.number_of_node_columns
# propid should be either a reference to a CA model's "property id"
# array, or None
self.propid = propid
self.prop_data = prop_data
self.prop_reset_value = prop_reset_value
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, grid_shape,
cts_type):
"""Create the grid and the field containing node states."""
if cts_type == 'raster' or cts_type == 'oriented_raster':
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
spacing=1.0)
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(num_rows, num_cols, 1.0,
orientation=grid_orientation,
shape=grid_shape)
self.grid.add_zeros('node', 'node_state', dtype=int)
class HexLatticeTectonicizer(object):
"""Base class from which classes to represent particular baselevel/fault
geometries are derived.
"""
def __init__(self, grid=None, node_state=None):
# If needed, create grid
if grid is None:
num_rows = _DEFAULT_NUM_ROWS
num_cols = _DEFAULT_NUM_COLS
self.grid = HexModelGrid(num_rows, num_cols, dx=1.0,
orientation='vertical',
shape='rect', reorient_links=True)
else:
# Make sure caller passed the right type of grid
assert (grid.orientation == 'vertical'), \
'Grid must have vertical orientation'
# Keep a reference to the grid
self.grid = grid
# If needed, create node-state grid
if node_state is None:
self.node_state = self.grid.add_zeros('node', 'node_state_map')
else:
self.node_state = node_state
# Remember the # of rows and cols
self.nr = self.grid.number_of_node_rows
self.nc = self.grid.number_of_node_columns
def __init__(self, grid=None, node_state=None):
# If needed, create grid
if grid is None:
num_rows = _DEFAULT_NUM_ROWS
num_cols = _DEFAULT_NUM_COLS
self.grid = HexModelGrid(num_rows, num_cols, dx=1.0,
orientation='vertical',
shape='rect', reorient_links=True)
else:
# Make sure caller passed the right type of grid
assert (grid.orientation == 'vertical'), \
'Grid must have vertical orientation'
# Keep a reference to the grid
self.grid = grid
# If needed, create node-state grid
if node_state is None:
self.node_state = self.grid.add_zeros('node', 'node_state_map')
else:
self.node_state = node_state
# Remember the # of rows and cols
self.nr = self.grid.number_of_node_rows
self.nc = self.grid.number_of_node_columns
def test_move_reference_hex(random_xy, n_rows, n_cols, shape, orientation):
mg = HexModelGrid(
n_rows,
n_cols,
dx=2.0,
xy_of_lower_left=random_xy,
orientation=orientation,
shape=shape,
)
assert mg.xy_of_lower_left == random_xy
assert mg.x_of_node.min() == random_xy[0]
assert mg.y_of_node.min() == random_xy[1]
mg.xy_of_lower_left = (30.0, 45.0)
assert mg._xy_of_lower_left == (30.0, 45.0)
assert mg.x_of_node.min() == approx(30.0)
assert mg.y_of_node.min() == approx(45.0)
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, grid_shape,
cts_type):
"""Create the grid and the field containing node states."""
if cts_type == 'raster' or cts_type == 'oriented_raster':
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
spacing=1.0)
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(num_rows,
num_cols,
1.0,
orientation=grid_orientation,
shape=grid_shape)
self.grid.add_zeros('node', 'node_state', dtype=int)
def test_nodes_at_link():
"""Test nodes_at_link shares data with tail and head."""
grid = HexModelGrid((3, 2))
assert_array_equal(grid.nodes_at_link[:, 0], grid.node_at_link_tail)
assert_array_equal(grid.nodes_at_link[:, 1], grid.node_at_link_head)
assert np.may_share_memory(grid.nodes_at_link, grid.node_at_link_tail)
assert np.may_share_memory(grid.nodes_at_link, grid.node_at_link_head)
def __init__(
self,
grid=None,
node_state=None,
propid=None,
prop_data=None,
prop_reset_value=None,
):
"""
Create and initialize a HexLatticeTectonicizer.
Examples
--------
>>> from landlab import HexModelGrid
>>> hg = HexModelGrid(6, 6, shape='rect')
>>> hlt = HexLatticeTectonicizer()
>>> hlt.grid.number_of_nodes
25
>>> hlt.nr
5
>>> hlt.nc
5
"""
# If needed, create grid
if grid is None:
num_rows = _DEFAULT_NUM_ROWS
num_cols = _DEFAULT_NUM_COLS
self.grid = HexModelGrid(
num_rows,
num_cols,
dx=1.0,
orientation="vertical",
shape="rect",
reorient_links=True,
)
else:
# Make sure caller passed the right type of grid
assert grid.orientation == "vertical", "Grid must have vertical orientation"
# Keep a reference to the grid
self.grid = grid
# If needed, create node-state grid
if node_state is None:
self.node_state = self.grid.add_zeros("node", "node_state_map", dtype=int)
else:
self.node_state = node_state
# Remember the # of rows and cols
self.nr = self.grid.number_of_node_rows
self.nc = self.grid.number_of_node_columns
# propid should be either a reference to a CA model's "property id"
# array, or None
self.propid = propid
self.prop_data = prop_data
self.prop_reset_value = prop_reset_value
def test_hex_cts():
"""Tests instantiation of a HexCTS() object"""
mg = HexModelGrid(
(3, 2),
spacing=1.0,
orientation="vertical",
node_layout="hex",
# reorient_links=True,
)
nsd = {0: "zero", 1: "one"}
xnlist = []
xnlist.append(Transition((0, 1, 0), (1, 1, 0), 1.0, "transitioning"))
nsg = mg.add_zeros("node_state_grid", at="node")
hcts = HexCTS(mg, nsd, xnlist, nsg)
assert hcts.num_link_states == 4
assert_array_equal(hcts.link_orientation,
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_shift_link_and_transition_data_upward():
"""Test the LatticeUplifter method that uplifts link data and tr'ns."""
mg = HexModelGrid((4, 3),
spacing=1.0,
orientation="vertical",
node_layout="rect")
nsd = {0: "yes", 1: "no"}
xnlist = []
xnlist.append(Transition((0, 0, 0), (1, 1, 0), 1.0, "frogging"))
xnlist.append(Transition((0, 0, 1), (1, 1, 1), 1.0, "frogging"))
xnlist.append(Transition((0, 0, 2), (1, 1, 2), 1.0, "frogging"))
nsg = mg.add_zeros("node_state_grid", at="node")
ohcts = OrientedHexCTS(mg, nsd, xnlist, nsg)
assert_array_equal(ohcts.link_state[mg.active_links],
[0, 4, 8, 8, 4, 0, 4, 8, 8, 4, 0])
assert_array_equal(ohcts.next_trn_id[mg.active_links],
[0, 1, 2, 2, 1, 0, 1, 2, 2, 1, 0])
assert_array_equal(
np.round(ohcts.next_update[mg.active_links], 2),
[0.8, 1.26, 0.92, 0.79, 0.55, 1.04, 0.58, 2.22, 3.31, 0.48, 1.57],
)
pq = ohcts.priority_queue
assert_equal(pq._queue[0][2], 19) # link for first event = 19, not shifted
assert_equal(round(pq._queue[0][0], 2), 0.48) # trn scheduled for t = 0.48
assert_equal(pq._queue[2][2], 14) # this event scheduled for link 15...
assert_equal(round(pq._queue[2][0], 2), 0.58) # ...trn sched for t = 0.58
lu = LatticeUplifter(grid=mg)
lu.shift_link_and_transition_data_upward(ohcts, 0.0)
# note new events lowest 5 links
assert_array_equal(
np.round(ohcts.next_update[mg.active_links], 2),
[0.75, 0.84, 2.6, 0.07, 0.09, 0.8, 0.02, 1.79, 1.51, 2.04, 3.85],
)
assert_equal(pq._queue[0][2], 14) # new soonest event
assert_equal(pq._queue[9][2], 13) # was previously 7, now shifted up...
assert_equal(round(pq._queue[9][0], 2), 0.8) # ...still sched for t = 0.80
def test_outlet_lowering_object_with_scaling():
"""Test using an outlet lowering object with scaling."""
mg = HexModelGrid(5, 5)
z = mg.add_zeros("node", "topographic__elevation")
node_id = 27
file = os.path.join(_TEST_DATA_DIR, "outlet_history.txt")
bh = SingleNodeBaselevelHandler(
mg,
outlet_id=node_id,
lowering_file_path=file,
model_end_elevation=-318.0,
)
for _ in range(241):
bh.run_one_step(10)
assert bh.z[node_id] == -95.0
assert z[1] == 0.0
def test_shift_link_and_transition_data_upward():
"""Test the LatticeUplifter method that uplifts link data and tr'ns."""
mg = HexModelGrid(4, 3, 1.0, orientation="vertical", shape="rect")
nsd = {0: "yes", 1: "no"}
xnlist = []
xnlist.append(Transition((0, 0, 0), (1, 1, 0), 1.0, "frogging"))
xnlist.append(Transition((0, 0, 1), (1, 1, 1), 1.0, "frogging"))
xnlist.append(Transition((0, 0, 2), (1, 1, 2), 1.0, "frogging"))
nsg = mg.add_zeros("node", "node_state_grid")
ohcts = OrientedHexCTS(mg, nsd, xnlist, nsg)
assert_array_equal(
ohcts.link_state[mg.active_links], [0, 4, 8, 8, 4, 0, 4, 8, 8, 4, 0]
)
assert_array_equal(
ohcts.next_trn_id[mg.active_links], [0, 1, 2, 2, 1, 0, 1, 2, 2, 1, 0]
)
assert_array_equal(
np.round(ohcts.next_update[mg.active_links], 2),
[0.8, 1.26, 0.92, 0.79, 0.55, 1.04, 0.58, 2.22, 3.31, 0.48, 1.57],
)
pq = ohcts.priority_queue
assert_equal(pq._queue[0][2], 20) # link for first event = 20, not shifted
assert_equal(round(pq._queue[0][0], 2), 0.48) # trn scheduled for t = 0.48
assert_equal(pq._queue[2][2], 15) # this event scheduled for link 15...
assert_equal(round(pq._queue[2][0], 2), 0.58) # ...trn sched for t = 0.58
lu = LatticeUplifter(grid=mg)
lu.shift_link_and_transition_data_upward(ohcts, 0.0)
# note new events lowest 5 links
assert_array_equal(
np.round(ohcts.next_update[mg.active_links], 2),
[0.75, 0.84, 2.6, 0.07, 0.09, 0.8, 0.02, 1.79, 1.51, 2.04, 3.85],
)
assert_equal(pq._queue[0][2], 15) # new soonest event
assert_equal(pq._queue[9][2], 14) # was previously 7, now shifted up...
assert_equal(round(pq._queue[9][0], 2), 0.8) # ...still sched for t = 0.80
def test_move_reference_hex(random_xy, n_rows, n_cols, node_layout,
orientation):
mg = HexModelGrid(
n_rows,
n_cols,
dx=2.0,
xy_of_lower_left=random_xy,
orientation=orientation,
node_layout=node_layout,
)
assert mg.xy_of_lower_left == random_xy
assert mg.x_of_node.min() == random_xy[0]
assert mg.y_of_node.min() == random_xy[1]
mg.xy_of_lower_left = (30.0, 45.0)
assert mg._xy_of_lower_left == (30.0, 45.0)
assert mg.x_of_node.min() == approx(30.0)
assert mg.y_of_node.min() == approx(45.0)
def test_hex():
"""Test using a hex grid."""
mg = HexModelGrid((5, 5))
z = mg.add_zeros("node", "topographic__elevation")
bh = NotCoreNodeBaselevelHandler(
mg, modify_core_nodes=False, lowering_rate=-0.1
)
bh.run_one_step(10.0)
closed = mg.status_at_node != 0
not_closed = mg.status_at_node == 0
# closed should have been downdropped 10*0.1
assert_array_equal(z[closed], -1.0 * np.ones(np.sum(closed)))
# not closed should have stayed the same
assert_array_equal(z[not_closed], np.zeros(np.sum(not_closed)))
def test_can_run_with_hex():
"""Test that model can run with hex model grid."""
# Set up a 5x5 grid with open boundaries and low initial elevations.
mg = HexModelGrid(7, 7)
z = mg.add_zeros('node', 'topographic__elevation')
z[:] = 0.01 * mg.x_of_node
# Create a D8 flow handler
fa = FlowAccumulator(mg, flow_director='FlowDirectorSteepest')
# Parameter values for test 1
K = 0.001
vs = 0.0001
U = 0.001
dt = 10.0
# Create the ErosionDeposition component...
ed = ErosionDeposition(mg,
K=K,
phi=0.0,
v_s=vs,
m_sp=0.5,
n_sp=1.0,
solver='adaptive')
# ... and run it to steady state.
for i in range(2000):
fa.run_one_step()
ed.run_one_step(dt=dt)
z[mg.core_nodes] += U * dt
# Test the results
s = mg.at_node['topographic__steepest_slope']
sa_factor = (1.0 + vs) * U / K
a18 = mg.at_node['drainage_area'][18]
a28 = mg.at_node['drainage_area'][28]
s = mg.at_node['topographic__steepest_slope']
s18 = sa_factor * (a18**-0.5)
s28 = sa_factor * (a28**-0.5)
testing.assert_equal(np.round(s[18], 3), np.round(s18, 3))
testing.assert_equal(np.round(s[28], 3), np.round(s28, 3))
def test_shape_dep_warning():
"""Test dep warning on use of shape keyword instead of node_layout."""
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger the deprecation warning.
HexModelGrid(3, 2, shape="rect")
# Verify some things
assert len(w) == 1
assert issubclass(w[-1].category, DeprecationWarning)
assert "node_layout" in str(w[-1].message)
def test_outlet_lowering_rate_on_not_outlet():
"""Test using an rate lowering object with no scaling and bedrock."""
mg = HexModelGrid(5, 5)
z = mg.add_ones("node", "topographic__elevation")
b = mg.add_zeros("node", "bedrock__elevation")
node_id = 27
bh = SingleNodeBaselevelHandler(
mg, outlet_id=node_id, lowering_rate=-0.1, modify_outlet_id=False
)
for _ in range(240):
bh.run_one_step(10)
assert z[node_id] == 1.0
assert b[node_id] == 0.0
not_outlet = mg.nodes != node_id
assert np.all(z[not_outlet] == 241.0)
assert np.all(b[not_outlet] == 240.0)
def test_outlet_lowering_object_no_scaling():
"""Test using an outlet lowering object with no scaling."""
mg = HexModelGrid((5, 5))
z = mg.add_ones("node", "topographic__elevation")
file = os.path.join(_TEST_DATA_DIR, "outlet_history.txt")
bh = NotCoreNodeBaselevelHandler(
mg, modify_core_nodes=False, lowering_file_path=file
)
for _ in range(241):
bh.run_one_step(10)
closed = mg.status_at_node != 0
not_closed = mg.status_at_node == 0
# not closed should have stayed the same
assert_array_equal(z[not_closed], np.ones(np.sum(not_closed)))
# closed should lowered by 47.5 to -46.5
assert_array_equal(z[closed], -46.5 * np.ones(np.sum(closed)))
def test_not_passing_infiltration_capacity():
mg = HexModelGrid(5, 5)
with pytest.raises(ValueError):
PrecipChanger(
mg,
daily_rainfall__intermittency_factor=0.3,
daily_rainfall__intermittency_factor_time_rate_of_change=0.001,
rainfall__mean_rate=3.0,
rainfall__mean_rate_time_rate_of_change=0.2,
rainfall__shape_factor=0.65,
)
def test_links_to_update():
"""Test that update list includes lower 2 rows and fault-crossing links"""
# Create a 6x6 test grid
hg = HexModelGrid((6, 6), node_layout="rect", orientation="vertical")
lnf = LatticeNormalFault(grid=hg, fault_x_intercept=-0.1)
assert_array_equal(
lnf.links_to_update,
[
6,
7,
9,
10,
11,
12,
13,
14,
16,
17,
18,
19,
20,
22,
23,
24,
25,
26,
27,
28,
29,
30,
33,
34,
35,
36,
38,
39,
41,
44,
49,
52,
54,
58,
60,
66,
68,
71,
74,
75,
78,
],
)
def test_links_to_update():
"""Test that update list includes lower 2 rows and fault-crossing links"""
# Create a 6x6 test grid
hg = HexModelGrid(6, 6, shape="rect", orientation="vert")
lnf = LatticeNormalFault(grid=hg, fault_x_intercept=-0.1)
assert_array_equal(
lnf.links_to_update,
[
8,
9,
11,
12,
13,
14,
15,
16,
18,
19,
20,
21,
22,
24,
25,
26,
27,
28,
29,
30,
31,
32,
35,
36,
37,
38,
40,
41,
43,
46,
51,
54,
56,
60,
62,
68,
70,
73,
76,
77,
80,
],
)
def test_hex_lower_left_as_iterables(random_xy, to_iterable):
expected = approx(tuple(random_xy))
grid = HexModelGrid(
(9, 5),
xy_of_lower_left=to_iterable(random_xy),
orientation="horizontal",
node_layout="rect",
)
assert isinstance(grid.xy_of_lower_left, tuple)
assert grid.xy_of_lower_left == expected
def test_outlet_lowering_object_no_scaling_bedrock():
"""Test using an outlet lowering object with no scaling and bedrock."""
mg = HexModelGrid(5, 5)
z = mg.add_ones("node", "topographic__elevation")
b = mg.add_zeros("node", "bedrock__elevation")
node_id = 27
file = os.path.join(_TEST_DATA_DIR, "outlet_history.txt")
bh = SingleNodeBaselevelHandler(
mg, outlet_id=node_id, lowering_file_path=file
)
for _ in range(241):
bh.run_one_step(10)
assert z[1] == 1.0
assert b[1] == 0.0
assert z[node_id] == -46.5
assert b[node_id] == -47.5
def test_non_raster():
"""Test a hex model grid."""
grid = HexModelGrid(7, 3, dx=10)
_ = grid.add_zeros('node', 'topographic__elevation')
param_dict = {
'faulted_surface': 'topographic__elevation',
'fault_dip_angle': 90.0,
'fault_throw_rate_through_time': {
'time': [0, 9, 10],
'rate': [0, 0, 0.05]
},
'fault_trace': {
'y1': 30.0,
'x1': 30.0,
'y2': 20.0,
'x2': 0.0
},
'include_boundaries': True
}
nf = NormalFault(grid, **param_dict)
# plotting, to test this. it works!
#import matplotlib.pyplot as plt
#plt.figure()
#imshow_grid(grid, nf.faulted_nodes, color_for_background='y')
#plt.plot(grid.x_of_node, grid.y_of_node, 'c.')
#plt.plot([param_dict['fault_trace']['x1'], param_dict['fault_trace']['x2']],
# [param_dict['fault_trace']['y1'], param_dict['fault_trace']['y2']], 'r')
#plt.show()
out = np.array([
True, True, True, True, True, True, True, False, True, True, True,
True, False, False, False, False, True, True, False, False, False,
False, False, False, False, False, False, False, False, False
],
dtype=bool)
assert_array_equal(nf.faulted_nodes, out)
def test_move_reference_hex(random_xy, n_rows, n_cols, node_layout,
orientation):
grid = HexModelGrid(
(n_rows, n_cols),
spacing=2.0,
xy_of_lower_left=random_xy,
orientation=orientation,
node_layout=node_layout,
)
assert grid.xy_of_lower_left == approx(random_xy)
assert grid.x_of_node.min() == approx(random_xy[0])
assert grid.y_of_node.min() == approx(random_xy[1])
x, y = grid.x_of_node.copy(), grid.y_of_node.copy()
grid.xy_of_lower_left = (30.0, 45.0)
assert grid.xy_of_lower_left == (30.0, 45.0)
assert grid.x_of_node - x == approx(30.0 - random_xy[0])
assert grid.y_of_node - y == approx(45.0 - random_xy[1])
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, node_layout,
cts_type):
"""Create the grid and the field containing node states."""
if cts_type == "raster" or cts_type == "oriented_raster":
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
xy_spacing=1.0)
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(
(num_rows, num_cols),
spacing=1.0,
orientation=grid_orientation,
node_layout=node_layout,
)
self.grid.add_zeros("node_state", at="node", dtype=int)
def create_grid_and_node_state_field(
self, num_rows, num_cols, grid_orientation, node_layout, cts_type
):
"""Create the grid and the field containing node states."""
if cts_type == "raster" or cts_type == "oriented_raster":
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols), xy_spacing=1.0)
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(
num_rows,
num_cols,
xy_spacing=1.0,
orientation=grid_orientation,
node_layout=node_layout,
)
self.grid.add_zeros("node", "node_state", dtype=int)
def test_shape_dep_warning():
"""Test dep warning on use of shape keyword instead of node_layout."""
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger the deprecation warning.
HexModelGrid(3, 2, shape="rect")
# Verify some things
catmsg = ""
for warn in w:
catmsg += str(warn.message)
assert "node_layout" in catmsg
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, grid_shape,
cts_type):
"""Create the grid and the field containing node states."""
if cts_type == 'raster' or cts_type == 'oriented_raster':
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
spacing=1.0)
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(num_rows,
num_cols,
1.0,
orientation=grid_orientation,
shape=grid_shape)
self.grid.add_zeros('node', 'node_state', dtype=int)
for edge in (self.grid.nodes_at_right_edge,
self.grid.nodes_at_top_edge):
self.grid.status_at_node[edge] = CLOSED_BOUNDARY
def test_can_run_with_hex():
"""Test that model can run with hex model grid."""
# Set up a 5x5 grid with open boundaries and low initial elevations.
mg = HexModelGrid(7, 7)
z = mg.add_zeros('node', 'topographic__elevation')
z[:] = 0.01 * mg.x_of_node
# Create a D8 flow handler
fa = FlowAccumulator(mg, flow_director='FlowDirectorSteepest')
# Parameter values for test 1
K = 0.001
vs = 0.0001
U = 0.001
dt = 10.0
# Create the ErosionDeposition component...
ed = ErosionDeposition(mg, K=K, phi=0.0, v_s=vs, m_sp=0.5, n_sp=1.0,
method='simple_stream_power',
discharge_method='drainage_area',
area_field='drainage_area',
solver='adaptive')
# ... and run it to steady state.
for i in range(2000):
fa.run_one_step()
ed.run_one_step(dt=dt)
z[mg.core_nodes] += U * dt
# Test the results
s = mg.at_node['topographic__steepest_slope']
sa_factor = (1.0 + vs) * U / K
a18 = mg.at_node['drainage_area'][18]
a28 = mg.at_node['drainage_area'][28]
s = mg.at_node['topographic__steepest_slope']
s18 = sa_factor * (a18 ** -0.5)
s28 = sa_factor * (a28 ** -0.5)
assert_equal(np.round(s[18], 3), np.round(s18, 3))
assert_equal(np.round(s[28], 3), np.round(s28, 3))
def test_can_run_with_hex():
"""Test that model can run with hex model grid."""
# Set up a 5x5 grid with open boundaries and low initial elevations.
mg = HexModelGrid(7, 7)
z = mg.add_zeros('node', 'topographic__elevation')
z[:] = 0.01 * mg.x_of_node
# Create a D8 flow handler
fa = FlowAccumulator(mg, flow_director='FlowDirectorSteepest')
# Parameter values for test 1
K = 0.001
vs = 0.0001
U = 0.001
dt = 10.0
# Create the ErosionDeposition component...
sp = Space(mg,
K_sed=0.00001,
K_br=0.00000000001,
F_f=0.5,
phi=0.1,
H_star=1.,
v_s=0.001,
m_sp=0.5,
n_sp=1.0,
sp_crit_sed=0,
sp_crit_br=0,
method='simple_stream_power',
discharge_method=None,
area_field=None,
discharge_field=None)
# ... and run it to steady state.
for i in range(2000):
fa.run_one_step()
sp.run_one_step(dt=dt)
z[mg.core_nodes] += U * dt
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, grid_shape,
cts_type, closed_bounds):
"""Create the grid and the field containing node states."""
if cts_type == 'raster' or cts_type == 'oriented_raster':
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
spacing=1.0)
self.grid.set_closed_boundaries_at_grid_edges(closed_bounds[0],
closed_bounds[1],
closed_bounds[2],
closed_bounds[3])
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(num_rows, num_cols, 1.0,
orientation=grid_orientation,
shape=grid_shape)
if True in closed_bounds:
self._set_closed_boundaries_for_hex_grid(closed_bounds)
self.grid.add_zeros('node', 'node_state', dtype=int)
def test_hex_grid_link_order():
"""Test the order of links in a small hex grid."""
grid = HexModelGrid((3, 2))
assert_array_equal(
grid.nodes_at_link,
[
[0, 1],
[0, 2],
[0, 3],
[1, 3],
[1, 4],
[2, 3],
[3, 4],
[2, 5],
[3, 5],
[3, 6],
[4, 6],
[5, 6],
],
)
grid = HexModelGrid((2, 3), orientation="vertical")
assert_array_equal(
grid.nodes_at_link,
[
[1, 0],
[0, 2],
[0, 3],
[1, 3],
[3, 2],
[1, 4],
[2, 5],
[4, 3],
[3, 5],
[3, 6],
[4, 6],
[6, 5],
],
)
def create_grid_and_node_state_field(self, num_rows, num_cols,
grid_orientation, node_layout,
cts_type, closed_bounds):
"""Create the grid and the field containing node states."""
if cts_type == 'raster' or cts_type == 'oriented_raster':
from landlab import RasterModelGrid
self.grid = RasterModelGrid(shape=(num_rows, num_cols),
spacing=1.0)
self.grid.set_closed_boundaries_at_grid_edges(
closed_bounds[0], closed_bounds[1], closed_bounds[2],
closed_bounds[3])
else:
from landlab import HexModelGrid
self.grid = HexModelGrid(shape=(num_rows, num_cols),
spacing=1.0,
orientation=grid_orientation,
node_layout=node_layout)
if True in closed_bounds:
self._set_closed_boundaries_for_hex_grid(closed_bounds)
self.grid.add_zeros('node', 'node_state', dtype=int)
def test_grid_from_dict_hex(orientation, node_layout, xy_of_lower_left):
kwds = dict(shape=(3, 4))
if orientation is not None:
kwds["orientation"] = orientation
if node_layout is not None:
kwds["node_layout"] = node_layout
if xy_of_lower_left is not None:
kwds["xy_of_lower_left"] = xy_of_lower_left
expected = HexModelGrid(**kwds)
actual = grid_from_dict("HexModelGrid", kwds)
assert_array_almost_equal(expected.x_of_node, actual.x_of_node)
assert_array_almost_equal(expected.y_of_node, actual.y_of_node)
def test_can_run_with_hex():
"""Test that model can run with hex model grid."""
# %%
# Set up a 5x5 grid with open boundaries and low initial elevations.
mg = HexModelGrid((7, 7))
z = mg.add_zeros("topographic__elevation", at="node")
_ = mg.add_zeros("soil__depth", at="node")
z[:] = 0.01 * mg.x_of_node
# Create a D8 flow handler
fa = FlowAccumulator(mg, flow_director="FlowDirectorSteepest")
# Parameter values for test 1
U = 0.001
dt = 10.0
# Create the SpaceLargeScaleEroder component...
sp = SpaceLargeScaleEroder(
mg,
K_sed=0.00001,
K_br=0.00000000001,
F_f=0.5,
phi=0.1,
H_star=1.0,
v_s=0.001,
m_sp=0.5,
n_sp=1.0,
sp_crit_sed=0,
sp_crit_br=0,
)
# ... and run it to steady state.
for _ in range(2000):
fa.run_one_step()
sp.run_one_step(dt=dt)
z[mg.core_nodes] += U * dt
def test_error_handling():
radial_grid = RadialModelGrid(
n_rings=1, nodes_in_first_ring=8) # , xy_of_center=(0., 0.))
assert_raises(TypeError, ListricKinematicExtender, radial_grid)
hex_grid = HexModelGrid((3, 3))
assert_raises(TypeError, ListricKinematicExtender, hex_grid)
grid = RasterModelGrid((3, 7))
grid.add_zeros("topographic__elevation", at="node")
assert_raises(KeyError,
ListricKinematicExtender,
grid,
track_crustal_thickness=True)
def test_flow__distance_irregular_grid_d4():
"""Test to demonstrate that flow__distance utility works as expected with irregular grids"""
# instantiate a model grid
dx = 1.0
hmg = HexModelGrid(5, 3, dx)
# instantiate and add the elevation field
hmg.add_field("topographic__elevation",
hmg.node_x + np.round(hmg.node_y),
at="node")
# instantiate the expected flow__distance array
flow__distance_expected = np.array([
0.0,
0.0,
0.0,
0.0,
0.0,
dx,
0.0,
0.0,
dx,
dx,
2.0 * dx,
0.0,
0.0,
2.0 * dx,
2.0 * dx,
0.0,
0.0,
0.0,
0.0,
])
# setting boundary conditions
hmg.set_closed_nodes(hmg.boundary_nodes)
# calculating flow directions with FlowAccumulator component: D4 algorithm
fr = FlowAccumulator(hmg, flow_director="D4")
fr.run_one_step()
# calculating flow distance map
flow__distance = calculate_flow__distance(hmg,
add_to_grid=True,
noclobber=False)
# test that the flow__distance utility works as expected
assert_almost_equal(flow__distance_expected, flow__distance, decimal=10)
def test_create_lnf(nr, nc):
pid = arange(nr * nc, dtype=int)
ns = arange(nr * nc, dtype=int)
pdata = arange(nr * nc)
grid = HexModelGrid(nr,
nc,
1.0,
orientation='vertical',
shape='rect',
reorient_links=True)
lnf = LatticeNormalFault(0.0, grid, ns, pid, pdata, 0.0)
#for i in range(grid.number_of_nodes):
# print i, grid.node_x[i], grid.node_y[i]
return lnf
def test_hex_model_grid(tmpdir, format, orientation, node_layout):
grid = HexModelGrid(
shape=(4, 5),
spacing=2.0,
xy_of_lower_left=(-3, -5),
orientation=orientation,
node_layout=node_layout,
)
with tmpdir.as_cwd():
to_netcdf(grid, "test.nc", format=format)
actual = from_netcdf("test.nc")
assert actual.spacing == grid.spacing
assert actual.xy_of_lower_left == grid.xy_of_lower_left
assert actual.orientation == grid.orientation
assert actual.node_layout == grid.node_layout
def test_hex_from_dict():
params = {
"base_num_rows": 5,
"base_num_cols": 4,
"dx": 2.0,
"xy_of_lower_left": (35, 55),
"axis_name": ("spam", "eggs"),
"axis_units": ("smoot", "parsec"),
"xy_of_reference": (12345, 678910),
}
mg = HexModelGrid.from_dict(params)
# assert things.
true_x_node = np.array(
[
37.0,
39.0,
41.0,
43.0,
36.0,
38.0,
40.0,
42.0,
44.0,
35.0,
37.0,
39.0,
41.0,
43.0,
45.0,
36.0,
38.0,
40.0,
42.0,
44.0,
37.0,
39.0,
41.0,
43.0,
]
)
assert_array_equal(true_x_node, mg.x_of_node)
assert (mg.x_of_node.min(), mg.y_of_node.min()) == (35, 55)
assert mg.axis_units == ("smoot", "parsec")
assert mg.axis_name == ("spam", "eggs")
assert mg.xy_of_reference == (12345, 678910)
def testing_flux_divergence_with_hex():
"""Test flux divergence function(s).
Notes
-----
Test grid looks like this:
(7)-17-.(8)-18-.(9)
. . . . . .
11 12 13 14 15 16
/ \ / \ / \
(3)--8-.(4)--9-.(5)-10-.(6)
. . . . . .
2 3 4 5 6 7
\ / \ / \ /
(0)--0-.(1)--1-.(2)
Node numbers in parentheses; others are link numbers; period indicates
link head.
"""
hmg = HexModelGrid(3, 3, reorient_links=True)
f = hmg.add_zeros('link', 'test_flux')
f[:] = np.arange(hmg.number_of_links)
make_links_at_node_array(hmg)
assert_array_equal(hmg.gt_num_links_at_node,
[3, 4, 3, 3, 6, 6, 3, 3, 4, 3])
assert_array_equal(hmg.gt_links_at_node,
[[ 0, 0, 1, 2, 3, 5, 7, 11, 13, 15],
[ 2, 1, 6, 8, 4, 6, 10, 12, 14, 16],
[ 3, 4, 7, 11, 8, 9, 16, 17, 17, 18],
[ -1, 5, -1, -1, 9, 10, -1, -1, 18, -1],
[ -1, -1, -1, -1, 12, 14, -1, -1, -1, -1],
[ -1, -1, -1, -1, 13, 15, -1, -1, -1, -1]])
assert_array_equal(hmg.gt_link_dirs_at_node,
[[ -1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[ -1, -1, -1, -1, 1, 1, 1, 1, 1, 1],
[ -1, -1, -1, -1, 1, 1, -1, -1, 1, 1],
[ 0, -1, 0, 0, -1, -1, 0, 0, -1, 0],
[ 0, 0, 0, 0, -1, -1, 0, 0, 0, 0],
[ 0, 0, 0, 0, -1, -1, 0, 0, 0, 0]])
raw_net_flux = np.zeros(hmg.number_of_nodes)
for r in range(MAX_NUM_LINKS):
raw_net_flux += f[hmg.gt_links_at_node[r,:]]*hmg.gt_link_dirs_at_node[r,:]
assert_array_equal(raw_net_flux,
[ -5., -10., -12., -17., -19., -19., 1., 6., 26., 49.])
nv = np.arange(hmg.number_of_nodes)
#gt_calc_gradients_at_faces(hmg, nv)
#gt_link_flux_divergence_at_cells_with_2darray(hmg, f)
# Some time trials
start = time.time()
for i in range(1000):
gt_grads_at_faces1(hmg, nv)
endtime = time.time()
def test_bad_init_gridmethod():
hmg = HexModelGrid(30, 29, dx=3.)
hmg.add_zeros("node", "topographic__elevation", dtype=float)
with pytest.raises(ValueError):
LakeMapperBarnes(hmg, method="D8")
def test_non_raster():
"""Test a hex model grid."""
grid = HexModelGrid(7, 3, dx=10, xy_of_lower_left=(-15.0, 0.0))
grid.add_zeros("node", "topographic__elevation")
param_dict = {
"faulted_surface": "topographic__elevation",
"fault_dip_angle": 90.0,
"fault_throw_rate_through_time": {"time": [0, 9, 10], "rate": [0, 0, 0.05]},
"fault_trace": {"y1": 30.0, "x1": 30.0, "y2": 20.0, "x2": 0.0},
"include_boundaries": True,
}
nf = NormalFault(grid, **param_dict)
# plotting, to test this. it works!
# import matplotlib.pyplot as plt
# plt.figure()
# imshow_grid(grid, nf.faulted_nodes, color_for_background='y')
# plt.plot(grid.x_of_node, grid.y_of_node, 'c.')
# plt.plot([param_dict['fault_trace']['x1'], param_dict['fault_trace']['x2']],
# [param_dict['fault_trace']['y1'], param_dict['fault_trace']['y2']], 'r')
# plt.show()
out = np.array(
[
True,
True,
True,
True,
True,
True,
True,
False,
True,
True,
True,
True,
False,
False,
False,
False,
True,
True,
False,
False,
False,
False,
False,
False,
False,
False,
False,
False,
False,
False,
],
dtype=bool,
)
assert_array_equal(nf.faulted_nodes, out)
def main():
"""
In this simple tutorial example, the main function does all the work:
it sets the parameter values, creates and initializes a grid, sets up
the state variables, runs the main loop, and cleans up.
"""
# INITIALIZE
# User-defined parameter values
numrows = 7 # number of rows in the grid
basenumcols = 6 # number of columns in the grid
dx = 10.0 # grid cell spacing
kd = 0.01 # diffusivity coefficient, in m2/yr
uplift_rate = 0.001 # baselevel/uplift rate, in m/yr
num_time_steps = 1000 # number of time steps in run
# Derived parameters
dt = 0.1*dx**2 / kd # time-step size set by CFL condition
# Create and initialize a raster model grid
mg = HexModelGrid(numrows, basenumcols, dx)
# Set up scalar values: elevation and elevation time derivative
z = mg.add_zeros('node', 'Land_surface__elevation')
dzdt = mg.add_zeros('node', 'Land_surface__time_derivative_of_elevation')
# Get a list of the core nodes
core_nodes = mg.core_nodes
# Display a message
print( 'Running diffusion_with_model_hex_grid.py' )
print( 'Time-step size has been set to ' + str( dt ) + ' years.' )
start_time = time.time()
# RUN
# Main loop
for i in range(0, num_time_steps):
# Calculate the gradients and sediment fluxes
g = mg.calculate_gradients_at_active_links(z)
qs = -kd*g
# Calculate the net deposition/erosion rate at each node
dqsds = mg.calculate_flux_divergence_at_nodes(qs)
# Calculate the total rate of elevation change
dzdt = uplift_rate - dqsds
# Update the elevations
z[core_nodes] = z[core_nodes] + dzdt[core_nodes] * dt
# FINALIZE
import numpy
# Test solution for a 1-cell hex grid
if mg.number_of_nodes==7: # single cell with 6 boundaries
perimeter = dx*6*(numpy.sqrt(3.)/3.)
flux = kd*(numpy.amax(z)/dx)
total_outflux = perimeter*flux
total_influx = mg.cell_areas*uplift_rate # just one cell ...
print 'total influx=',total_influx,'total outflux=',total_outflux
print('Run time = '+str(time.time()-start_time)+' seconds')
# Plot the points, colored by elevation
pylab.figure()
maxelev = numpy.amax(z)
for i in range(mg.number_of_nodes):
mycolor = str(z[i]/maxelev)
pylab.plot(mg.node_x[i], mg.node_y[i], 'o', color=mycolor, ms=50)
pylab.show()
mg.display_grid()
def test_hex_mfd():
mg = HexModelGrid(5, 3)
mg.add_field("topographic__elevation", mg.node_x + mg.node_y, at="node")
fa = LossyFlowAccumulator(mg, flow_director="MFD")
fa.run_one_step()
def main():
# INITIALIZE
# User-defined parameters
nr = 80 # number of rows in grid
nc = 50 # number of columns in grid
plot_interval = 0.5 # time interval for plotting, sec
run_duration = 20.0 # duration of run, sec
report_interval = 10.0 # report interval, in real-time seconds
# Remember the clock time, and calculate when we next want to report
# progress.
current_real_time = time.time()
next_report = current_real_time + report_interval
# Create grid
mg = HexModelGrid(nr, nc, 1.0)
# Make the boundaries be walls
# mg.set_closed_boundaries_at_grid_edges(True, True, True, True)<--I am not sure what the equivalent is for hexgrid
#Create a node-state dictionary
ns_dict = { 0 : 'fluid', 1 : 'particle' }
#Create the transition list
xn_list = setup_transition_list()
# Create the node-state array and attach it to the grid
node_state_grid = mg.add_zeros('node', 'node_state_map', dtype=int)
# Initialize the node-state array: here, the initial condition is a pile of
# resting grains at the bottom of a container.
bottom_rows = where(mg.node_y<0.1*nr)[0]
node_state_grid[bottom_rows] = 1
# For visual display purposes, set all boundary nodes to fluid
node_state_grid[mg.closed_boundary_nodes] = 0
# Create the CA model
ca = OrientedHexCTS(mg, ns_dict, xn_list, node_state_grid)
# Set up colors for plotting
grain = '#5F594D'
fluid = '#D0E4F2'
clist = [fluid,grain]
my_cmap = matplotlib.colors.ListedColormap(clist)
# Create a CAPlotter object for handling screen display
ca_plotter = CAPlotter(ca, cmap=my_cmap)
# Plot the initial grid
ca_plotter.update_plot()
# RUN
current_time = 0.0
while current_time < run_duration:
# Once in a while, print out simulation real time to let the user
# know that the sim is running ok
current_real_time = time.time()
if current_real_time >= next_report:
print('Current simulation time '+str(current_time)+' \
('+str(int(100*current_time/run_duration))+'%)')
next_report = current_real_time + report_interval
# Run the model forward in time until the next output step
ca.run(current_time+plot_interval, ca.node_state, plot_each_transition=False)
current_time += plot_interval
# Plot the current grid
ca_plotter.update_plot()
ca_plotter.finalize()
def main():
# INITIALIZE
# User-defined parameters
nr = 41
nc = 61
g = 0.8
f = 1.0
silo_y0 = 30.0
silo_opening_half_width = 6
plot_interval = 1.0
run_duration = 80.0
report_interval = 5.0 # report interval, in real-time seconds
p_init = 0.4 # probability that a cell is occupied at start
plot_every_transition = False
# Remember the clock time, and calculate when we next want to report
# progress.
current_real_time = time.time()
next_report = current_real_time + report_interval
# Create a grid
hmg = HexModelGrid(nr, nc, 1.0, orientation='vertical', reorient_links=True)
# Set up the states and pair transitions.
# Transition data here represent particles moving on a lattice: one state
# per direction (for 6 directions), plus an empty state, a stationary
# state, and a wall state.
ns_dict = { 0 : 'empty',
1 : 'moving up',
2 : 'moving right and up',
3 : 'moving right and down',
4 : 'moving down',
5 : 'moving left and down',
6 : 'moving left and up',
7 : 'rest',
8 : 'wall'}
xn_list = setup_transition_list(g, f)
# Create data and initialize values.
node_state_grid = hmg.add_zeros('node', 'node_state_grid')
# Make the grid boundary all wall particles
node_state_grid[hmg.boundary_nodes] = 8
# Place wall particles to form the base of the silo, initially closed
tan30deg = numpy.tan(numpy.pi/6.)
rampy1 = silo_y0-hmg.node_x*tan30deg
rampy2 = silo_y0-((nc*0.866-1.)-hmg.node_x)*tan30deg
rampy = numpy.maximum(rampy1, rampy2)
(ramp_nodes, ) = numpy.where(numpy.logical_and(hmg.node_y>rampy-0.5, \
hmg.node_y<rampy+0.5))
node_state_grid[ramp_nodes] = 8
# Seed the grid interior with randomly oriented particles
for i in hmg.core_nodes:
if hmg.node_y[i]>rampy[i] and random.random()<p_init:
node_state_grid[i] = random.randint(1, 7)
# Create the CA model
ca = OrientedHexLCA(hmg, ns_dict, xn_list, node_state_grid)
# Create a CAPlotter object for handling screen display
ca_plotter = CAPlotter(ca)
# Plot the initial grid
ca_plotter.update_plot()
# RUN
# Run with closed silo
current_time = 0.0
while current_time < run_duration:
# Once in a while, print out simulation and real time to let the user
# know that the sim is running ok
current_real_time = time.time()
if current_real_time >= next_report:
print 'Current sim time',current_time,'(',100*current_time/run_duration,'%)'
next_report = current_real_time + report_interval
# Run the model forward in time until the next output step
ca.run(current_time+plot_interval, ca.node_state,
plot_each_transition=plot_every_transition, plotter=ca_plotter)
current_time += plot_interval
# Plot the current grid
ca_plotter.update_plot()
# Open the silo
xmid = nc*0.866*0.5
for i in range(hmg.number_of_nodes):
if node_state_grid[i]==8 and hmg.node_x[i]>(xmid-silo_opening_half_width) \
and hmg.node_x[i]<(xmid+silo_opening_half_width) \
and hmg.node_y[i]>0:
node_state_grid[i]=0
# Create the CA model
ca = OrientedHexLCA(hmg, ns_dict, xn_list, node_state_grid)
# Create a CAPlotter object for handling screen display
ca_plotter = CAPlotter(ca)
# Plot the initial grid
ca_plotter.update_plot()
# Re-run with open silo
current_time = 0.0
while current_time < 5*run_duration:
# Once in a while, print out simulation and real time to let the user
# know that the sim is running ok
current_real_time = time.time()
if current_real_time >= next_report:
print 'Current sim time',current_time,'(',100*current_time/run_duration,'%)'
next_report = current_real_time + report_interval
# Run the model forward in time until the next output step
ca.run(current_time+plot_interval, ca.node_state,
plot_each_transition=plot_every_transition, plotter=ca_plotter)
current_time += plot_interval
# Plot the current grid
ca_plotter.update_plot()
# FINALIZE
# Plot
ca_plotter.finalize()
def main():
# INITIALIZE
# User-defined parameters
nr = 21
nc = 21
plot_interval = 0.5
run_duration = 25.0
report_interval = 5.0 # report interval, in real-time seconds
# Remember the clock time, and calculate when we next want to report
# progress.
current_real_time = time.time()
next_report = current_real_time + report_interval
# Create a grid
hmg = HexModelGrid(nr, nc, 1.0, orientation='vertical', reorient_links=True)
# Close the grid boundaries
hmg.set_closed_nodes(hmg.open_boundary_nodes)
# Set up the states and pair transitions.
# Transition data here represent the disease status of a population.
ns_dict = { 0 : 'fluid', 1 : 'grain' }
xn_list = setup_transition_list()
# Create data and initialize values. We start with the 3 middle columns full
# of grains, and the others empty.
node_state_grid = hmg.add_zeros('node', 'node_state_grid')
middle = 0.25*(nc-1)*sqrt(3)
is_middle_cols = logical_and(hmg.node_x<middle+1., hmg.node_x>middle-1.)
node_state_grid[where(is_middle_cols)[0]] = 1
# Create the CA model
ca = OrientedHexCTS(hmg, ns_dict, xn_list, node_state_grid)
# Create a CAPlotter object for handling screen display
ca_plotter = CAPlotter(ca)
# Plot the initial grid
ca_plotter.update_plot()
# RUN
current_time = 0.0
while current_time < run_duration:
# Once in a while, print out simulation and real time to let the user
# know that the sim is running ok
current_real_time = time.time()
if current_real_time >= next_report:
print('Current sim time',current_time,'(',100*current_time/run_duration,'%)')
next_report = current_real_time + report_interval
# Run the model forward in time until the next output step
ca.run(current_time+plot_interval, ca.node_state,
plot_each_transition=False)
current_time += plot_interval
# Plot the current grid
ca_plotter.update_plot()
# FINALIZE
# Plot
ca_plotter.finalize()