class GrainFacet(CTSModel):
"""
Model hillslope evolution with block uplift.
"""
def __init__(self,
grid_size,
report_interval=1.0e8,
run_duration=1.0,
output_interval=1.0e99,
settling_rate=2.2e8,
disturbance_rate=1.0,
weathering_rate=1.0,
uplift_interval=1.0,
plot_interval=1.0e99,
friction_coef=0.3,
fault_x=1.0,
rock_state_for_uplift=7,
opt_rock_collapse=False,
show_plots=True,
initial_state_grid=None,
opt_track_grains=False,
prop_data=None,
prop_reset_value=None,
callback_fn=None,
**kwds):
"""Call the initialize() method."""
self.initializer(grid_size, report_interval, run_duration,
output_interval, settling_rate, disturbance_rate,
weathering_rate, uplift_interval, plot_interval,
friction_coef, fault_x, rock_state_for_uplift,
opt_rock_collapse, show_plots, initial_state_grid,
opt_track_grains, prop_data, prop_reset_value,
callback_fn, **kwds)
def initializer(self, grid_size, report_interval, run_duration,
output_interval, settling_rate, disturbance_rate,
weathering_rate, uplift_interval, plot_interval,
friction_coef, fault_x, rock_state_for_uplift,
opt_rock_collapse, show_plots, initial_state_grid,
opt_track_grains, prop_data, prop_reset_value, callback_fn,
**kwds):
"""Initialize the grain hill model."""
self.settling_rate = settling_rate
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.uplift_interval = uplift_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
self.rock_state = rock_state_for_uplift # 7 (resting sed) or 8 (rock)
self.opt_track_grains = opt_track_grains
self.callback_fn = callback_fn
if opt_rock_collapse:
self.collapse_rate = self.settling_rate
else:
self.collapse_rate = 0.0
# Call base class init
super(GrainFacet,
self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=show_plots,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
initial_state_grid=initial_state_grid,
prop_data=prop_data,
prop_reset_value=prop_reset_value,
**kwds)
# Set some things related to property-swapping and/or callback fn
# if the user wants to track grain motion.
#if opt_track_grains:
# propid = self.ca.propid
#else:
# propid = None
self.uplifter = LatticeNormalFault(
fault_x_intercept=fault_x,
grid=self.grid,
node_state=self.grid.at_node['node_state'],
propid=self.ca.propid,
prop_data=self.ca.prop_data,
prop_reset_value=self.ca.prop_reset_value)
self.initialize_timing(output_interval, plot_interval, uplift_interval,
report_interval)
def initialize_timing(self, output_interval, plot_interval,
uplift_interval, report_interval):
"""Set up variables related to timing of uplift, output, reporting"""
self.current_time = 0.0
# Next time for output to file
self.next_output = output_interval
# Next time for a plot
if self._show_plots:
self.next_plot = plot_interval
else:
self.next_plot = self.run_duration + 1
# Next time for a progress report to user
self.next_report = report_interval
# Next time to add baselevel adjustment
self.next_uplift = uplift_interval
# Iteration numbers, for output files
self.output_iteration = 1
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=self.settling_rate,
f=self.friction_coef,
motion=self.settling_rate,
swap=self.opt_track_grains,
callback=self.callback_fn)
xn_list = self.add_weathering_and_disturbance_transitions(
xn_list,
self.disturbance_rate,
self.weathering_rate,
collapse_rate=self.collapse_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self,
xn_list,
d=0.0,
w=0.0,
collapse_rate=0.0,
swap=False,
callback=None):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
if d > 0.0:
xn_list.append(
Transition((7, 0, 0), (0, 1, 0), d, 'disturbance', swap,
callback))
xn_list.append(
Transition((7, 0, 1), (0, 2, 1), d, 'disturbance', swap,
callback))
xn_list.append(
Transition((7, 0, 2), (0, 3, 2), d, 'disturbance', swap,
callback))
xn_list.append(
Transition((0, 7, 0), (4, 0, 0), d, 'disturbance', swap,
callback))
xn_list.append(
Transition((0, 7, 1), (5, 0, 1), d, 'disturbance', swap,
callback))
xn_list.append(
Transition((0, 7, 2), (6, 0, 2), d, 'disturbance', swap,
callback))
# Weathering rule
if w > 0.0:
xn_list.append(Transition((8, 0, 0), (7, 0, 0), w, 'weathering'))
xn_list.append(Transition((8, 0, 1), (7, 0, 1), w, 'weathering'))
xn_list.append(Transition((8, 0, 2), (7, 0, 2), w, 'weathering'))
xn_list.append(Transition((0, 8, 0), (0, 7, 0), w, 'weathering'))
xn_list.append(Transition((0, 8, 1), (0, 7, 1), w, 'weathering'))
xn_list.append(Transition((0, 8, 2), (0, 7, 2), w, 'weathering'))
# "Vertical rock collapse" rule: a rock particle overlying air
# will collapse, transitioning to a downward-moving grain
if collapse_rate > 0.0:
xn_list.append(
Transition((0, 8, 0), (4, 0, 0), collapse_rate,
'rock collapse', swap, callback))
if _DEBUG:
print()
print('setup_transition_list(): list has ' + str(len(xn_list)) +
' transitions:')
for t in xn_list:
print(' From state ' + str(t.from_state) + ' to state ' +
str(t.to_state) + ' at rate ' + str(t.rate) +
' called ' + str(t.name))
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> gh = GrainFacet((5, 7))
>>> gh.grid.at_node['node_state']
array([8, 7, 7, 8, 7, 7, 7, 0, 7, 7, 0, 7, 7, 7, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 2.0:
if (self.grid.node_x[i] > 0.0
and self.grid.node_x[i] < right_side_x):
nsg[i] = 7
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def run(self, to=None):
"""Run the model."""
if to is None:
run_to = self.run_duration
else:
run_to = to
while self.current_time < run_to:
# Figure out what time to run to this iteration
next_pause = min(self.next_output, self.next_plot)
next_pause = min(next_pause, self.next_uplift)
next_pause = min(next_pause, run_to)
# 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 >= self.next_report:
print('Current sim time' + str(self.current_time) + '(' + \
str(100 * self.current_time / self.run_duration) + '%)')
self.next_report = current_real_time + self.report_interval
# Run until next pause
self.ca.run(next_pause, self.ca.node_state)
self.current_time = next_pause
# Handle output to file
if self.current_time >= self.next_output:
self.write_output(self.grid, 'grain_hill_model',
self.output_iteration)
self.output_iteration += 1
self.next_output += self.output_interval
# Handle plotting on display
if self._show_plots and self.current_time >= self.next_plot:
self.ca_plotter.update_plot()
axis('off')
self.next_plot += self.plot_interval
# Handle uplift
if self.current_time >= self.next_uplift:
self.uplifter.do_offset(ca=self.ca,
current_time=self.current_time,
rock_state=self.rock_state)
self.next_uplift += self.uplift_interval
def get_profile_and_soil_thickness(self, grid, data):
"""Calculate and return profiles of elevation and soil thickness.
Examples
--------
>>> from landlab import HexModelGrid
>>> hg = HexModelGrid(4, 5, shape='rect', orientation='vert')
>>> ns = hg.add_zeros('node', 'node_state', dtype=int)
>>> ns[[0, 3, 1, 6, 4, 9, 2]] = 8
>>> ns[[8, 13, 11, 16, 14]] = 7
>>> gh = GrainHill((3, 7)) # grid size arbitrary here
>>> (elev, thickness) = gh.get_profile_and_soil_thickness(hg, ns)
>>> elev
array([0. , 2.5, 3. , 2.5, 0. ])
>>> thickness
array([0., 2., 2., 1., 0.])
"""
nc = grid.number_of_node_columns
elev = zeros(nc)
soil = zeros(nc)
for col in range(nc):
states = data[grid.nodes[:, col]]
(rows_with_rock_or_sed, ) = where(states > 0)
if len(rows_with_rock_or_sed) == 0:
elev[col] = 0.0
else:
elev[col] = amax(rows_with_rock_or_sed) + 0.5 * (col % 2)
soil[col] = count_nonzero(logical_and(states > 0, states < 8))
return elev, soil
class GrainFacetSimulator(CTSModel):
"""
Model facet-slope evolution with 60-degree normal-fault slip.
"""
def __init__(self, grid_size, report_interval=1.0e8, run_duration=1.0,
output_interval=1.0e99, disturbance_rate=0.0,
weathering_rate=0.0, dissolution_rate=0.0,
uplift_interval=1.0, baselevel_rise_interval=0,
plot_interval=1.0e99, friction_coef=0.3,
fault_x=1.0, cell_width=1.0, grav_accel=9.8,
init_state_grid=None, save_plots=False, plot_filename=None,
plot_filetype='.png', seed=0, **kwds):
"""Call the initialize() method."""
self.initialize(grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
dissolution_rate, uplift_interval,
baselevel_rise_interval, plot_interval, friction_coef,
fault_x,cell_width, grav_accel, init_state_grid,
save_plots, plot_filename, plot_filetype, seed, **kwds)
def initialize(self, grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
dissolution_rate, uplift_interval, baselevel_rise_interval,
plot_interval, friction_coef, fault_x, cell_width,
grav_accel, init_state_grid=None, save_plots=False,
plot_filename=None, plot_filetype='.png', seed=0, **kwds):
"""Initialize the grain hill model."""
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.dissolution_rate = dissolution_rate
self.uplift_interval = uplift_interval
self.baselevel_rise_interval = baselevel_rise_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
self.settling_rate = calculate_settling_rate(cell_width, grav_accel)
# Call base class init
super(GrainFacetSimulator, self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=False,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
plot_every_transition=False,
initial_state_grid=init_state_grid,
closed_boundaries=(True, True,
False, False),
seed=seed)
ns = self.grid.at_node['node_state']
self.uplifter = LatticeNormalFault(fault_x_intercept=fault_x,
grid=self.grid,
node_state=ns)
# initialize plotting
if plot_interval <= run_duration:
import matplotlib.pyplot as plt
plt.ion()
plt.figure(1)
self.save_plots = save_plots
if save_plots:
self.plot_filename = plot_filename
self.plot_filetype = plot_filetype
nplots = (self.run_duration / self.plot_interval) + 1
self.ndigits = int(np.floor(np.log10(nplots))) + 1
this_filename = (plot_filename + '0'.zfill(self.ndigits)
+ plot_filetype)
print(this_filename)
else:
this_filename = None
plot_hill(self.grid, this_filename)
# Work out the next times to plot and output
self.next_output = self.output_interval
self.next_plot = self.plot_interval
self.plot_iteration = 1
# Next time for a progress report to user
self.next_report = self.report_interval
# And baselevel adjustment
self.next_uplift = self.uplift_interval
if self.baselevel_rise_interval > 0:
self.next_baselevel = self.baselevel_rise_interval
self.baselevel_row = 1
else:
self.next_baselevel = self.run_duration + 1
self.current_time = 0.0
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=self.settling_rate,
f=self.friction_coef,
motion=self.settling_rate)
xn_list = self.add_weathering_and_disturbance_transitions(xn_list,
self.disturbance_rate, self.weathering_rate,
self.dissolution_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self, xn_list, d=0.0, w=0.0,
diss=0.0):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional, default=0.0)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional, default=0.0)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
diss : float (optional, default=0.0)
Dissolution: rate of transition from fluid / rock pair to
fluid / fluid pair.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
if d > 0.0:
xn_list.append( Transition((7,0,0), (0,1,0), d, 'disturbance') )
xn_list.append( Transition((7,0,1), (0,2,1), d, 'disturbance') )
xn_list.append( Transition((7,0,2), (0,3,2), d, 'disturbance') )
xn_list.append( Transition((0,7,0), (4,0,0), d, 'disturbance') )
xn_list.append( Transition((0,7,1), (5,0,1), d, 'disturbance') )
xn_list.append( Transition((0,7,2), (6,0,2), d, 'disturbance') )
# Weathering rule
if w > 0.0:
xn_list.append( Transition((8,0,0), (7,0,0), w, 'weathering') )
xn_list.append( Transition((8,0,1), (7,0,1), w, 'weathering') )
xn_list.append( Transition((8,0,2), (7,0,2), w, 'weathering') )
xn_list.append( Transition((0,8,0), (0,7,0), w, 'weathering') )
xn_list.append( Transition((0,8,1), (0,7,1), w, 'weathering') )
xn_list.append( Transition((0,8,2), (0,7,2), w, 'weathering') )
# Dissolution rule
if diss > 0.0:
xn_list.append( Transition((8,0,0), (0,0,0), diss, 'dissolution') )
xn_list.append( Transition((8,0,1), (0,0,1), diss, 'dissolution') )
xn_list.append( Transition((8,0,2), (0,0,2), diss, 'dissolution') )
xn_list.append( Transition((0,8,0), (0,0,0), diss, 'dissolution') )
xn_list.append( Transition((0,8,1), (0,0,1), diss, 'dissolution') )
xn_list.append( Transition((0,8,2), (0,0,2), diss, 'dissolution') )
if _DEBUG:
print('')
print('setup_transition_list(): list has ' + str(len(xn_list))
+ ' transitions:')
for t in xn_list:
print(' From state ' + str(t.from_state) + ' to state '
+ str(t.to_state) + ' at rate ' + str(t.rate) + 'called'
+ str(t.name))
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> from grainhill import GrainHill
>>> gh = GrainHill((5, 7))
>>> gh.grid.at_node['node_state'][:20]
array([8, 7, 7, 8, 7, 7, 7, 0, 7, 7, 0, 7, 7, 7, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 2.0:
if (self.grid.node_x[i] > 0.0 and
self.grid.node_x[i] < right_side_x):
nsg[i] = 8
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def update_until(self, run_to_time):
"""Advance up to a specified time."""
while self.current_time < run_to_time:
# Figure out what time to run to this iteration
next_pause = min(self.next_output, self.next_plot)
next_pause = min(next_pause, self.next_uplift)
next_pause = min(next_pause, self.next_baselevel)
next_pause = min(next_pause, run_to_time)
# 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 >= self.next_report:
print('Current sim time ' + str(self.current_time) + ' (' + \
str(100 * self.current_time / self.run_duration) + '%)')
self.next_report = current_real_time + self.report_interval
# Run the model forward in time until the next output step
print('Running to...' + str(next_pause))
self.ca.run(next_pause, self.ca.node_state)
self.current_time = next_pause
# Handle output to file
if self.current_time >= self.next_output:
self.next_output += self.output_interval
# Handle plotting on display
if self.current_time >= self.next_plot:
if self.save_plots:
this_filename = (self.plot_filename
+ str(self.plot_iteration).zfill(self.ndigits)
+ self.plot_filetype)
else:
this_filename = None
plot_hill(self.grid, this_filename)
self.plot_iteration += 1
self.next_plot += self.plot_interval
# Handle fault slip
if self.current_time >= self.next_uplift:
self.uplifter.do_offset(ca=self.ca,
current_time=self.current_time,
rock_state=8)
# for i in range(self.grid.number_of_links):
# if self.grid.status_at_link[i] == 4 and self.ca.next_trn_id[i] != -1:
# print((i, self.ca.next_trn_id[i]))
# print((self.grid.x_of_node[self.grid.node_at_link_tail[i]]))
# print((self.grid.y_of_node[self.grid.node_at_link_tail[i]]))
# print((self.grid.x_of_node[self.grid.node_at_link_head[i]]))
# print((self.grid.y_of_node[self.grid.node_at_link_head[i]]))
self.next_uplift += self.uplift_interval
# Handle baselevel rise
if self.current_time >= self.next_baselevel:
self.raise_baselevel(self.baselevel_row)
self.baselevel_row += 1
self.next_baselevel += self.baselevel_rise_interval
def run(self, to=None):
"""Run the model."""
if to is None:
to = self.run_duration
self.update_until(to)
def raise_baselevel(self, baselevel_row):
"""Raise baselevel on left by closing a node on the left boundary.
Parameters
----------
baselevel_row : int
Row number of the next left-boundary node to be closed
Examples
--------
>>> params = { 'grid_size' : (10,5), 'baselevel_rise_interval' : 1.0 }
>>> params['run_duration'] = 10.0
>>> params['uplift_interval'] = 11.0
>>> gfs = GrainFacetSimulator(**params)
>>> gfs.run()
Current sim time 0.0 (0.0%)
Running to...1.0
Running to...2.0
Running to...3.0
Running to...4.0
Running to...5.0
Running to...6.0
Running to...7.0
Running to...8.0
Running to...9.0
Running to...10.0
>>> gfs.ca.node_state[:50:5]
array([8, 8, 8, 8, 8, 8, 8, 8, 8, 8])
"""
baselevel_node = self.grid.number_of_node_columns * baselevel_row
if baselevel_node < self.grid.number_of_nodes:
self.ca.node_state[baselevel_node] = 8
self.ca.bnd_lnk[self.grid.links_at_node[baselevel_node]] = True
self.grid.status_at_node[baselevel_node] = self.grid.BC_NODE_IS_CLOSED
def nodes_in_column(self, col, num_rows, num_cols):
"""Return array of node IDs in given column.
Examples
--------
>>> gfs = GrainFacetSimulator((3, 5))
>>> gfs.nodes_in_column(1, 3, 5)
array([ 3, 8, 13])
>>> gfs.nodes_in_column(4, 3, 5)
array([ 2, 7, 12])
>>> gfs = GrainFacetSimulator((3, 6))
>>> gfs.nodes_in_column(3, 3, 6)
array([ 4, 10, 16])
>>> gfs.nodes_in_column(4, 3, 6)
array([ 2, 8, 14])
"""
base_node = (col // 2) + (col % 2) * ((num_cols + 1) // 2)
num_nodes = num_rows * num_cols
return np.arange(base_node, num_nodes, num_cols)
def get_profile_and_soil_thickness(self):
"""Calculate and return the topographic profile and the regolith
thickness."""
nr = self.ca.grid.number_of_node_rows
nc = self.ca.grid.number_of_node_columns
data = self.ca.node_state
elev = np.zeros(nc)
soil = np.zeros(nc)
for c in range(nc):
e = (c%2)/2.0
s = 0
r = 0
while r<nr and data[c*nr+r]!=0:
e+=1
if data[c*nr+r]==7:
s+=1
r+=1
elev[c] = e
soil[c] = s
return elev, soil
def report_info_for_debug(self, current_time):
"""Print out various bits of data, for testing and debugging."""
print('\n Current time: ' + str(current_time))
print('Node state:')
print(self.ca.node_state)
for lnk in range(self.grid.number_of_links):
if self.grid.status_at_link[lnk] == 0:
print((lnk, self.grid.node_at_link_tail[lnk],
self.grid.node_at_link_head[lnk],
self.ca.node_state[self.grid.node_at_link_tail[lnk]],
self.ca.node_state[self.grid.node_at_link_head[lnk]],
self.ca.link_state[lnk],self.ca.next_update[lnk],
self.ca.next_trn_id[lnk]))
print('PQ:')
print(self.ca.priority_queue._queue)
def plot_to_file(self):
"""Plot profile of hill to file."""
fname = self.plot_file_name + str(self.plot_number).zfill(4) + '.png'
plot_hill(self.ca.grid, filename=fname)
self.plot_number += 1
class GrainFacet(CTSModel):
"""
Model hillslope evolution with block uplift.
"""
def __init__(self, grid_size, report_interval=1.0e8, run_duration=1.0,
output_interval=1.0e99, settling_rate=2.2e8,
disturbance_rate=1.0, weathering_rate=1.0,
uplift_interval=1.0, plot_interval=1.0e99, friction_coef=0.3,
fault_x=1.0,
rock_state_for_uplift=7, opt_rock_collapse=False,
show_plots=True, initial_state_grid=None,
opt_track_grains=False, prop_data=None,
prop_reset_value=None, callback_fn=None, **kwds):
"""Call the initialize() method."""
self.initializer(grid_size, report_interval, run_duration,
output_interval, settling_rate, disturbance_rate,
weathering_rate, uplift_interval, plot_interval,
friction_coef, fault_x, rock_state_for_uplift,
opt_rock_collapse, show_plots, initial_state_grid,
opt_track_grains, prop_data, prop_reset_value,
callback_fn, **kwds)
def initializer(self, grid_size, report_interval, run_duration,
output_interval, settling_rate, disturbance_rate,
weathering_rate, uplift_interval, plot_interval,
friction_coef, fault_x, rock_state_for_uplift, opt_rock_collapse,
show_plots, initial_state_grid, opt_track_grains, prop_data,
prop_reset_value, callback_fn, **kwds):
"""Initialize the grain hill model."""
self.settling_rate = settling_rate
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.uplift_interval = uplift_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
self.rock_state = rock_state_for_uplift # 7 (resting sed) or 8 (rock)
self.opt_track_grains = opt_track_grains
self.callback_fn = callback_fn
if opt_rock_collapse:
self.collapse_rate = self.settling_rate
else:
self.collapse_rate = 0.0
# Call base class init
super(GrainFacet, self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=show_plots,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
initial_state_grid=initial_state_grid,
prop_data=prop_data,
prop_reset_value=prop_reset_value,
**kwds)
# Close top and right edges so as to avoid boundary bug issue
for edge in (self.grid.nodes_at_right_edge,
self.grid.nodes_at_top_edge):
self.grid.status_at_node[edge] = CLOSED_BOUNDARY
# Set some things related to property-swapping and/or callback fn
# if the user wants to track grain motion.
#if opt_track_grains:
# propid = self.ca.propid
#else:
# propid = None
self.uplifter = LatticeNormalFault(fault_x_intercept=fault_x,
grid=self.grid,
node_state=self.grid.at_node['node_state'],
propid=self.ca.propid,
prop_data=self.ca.prop_data,
prop_reset_value=self.ca.prop_reset_value)
self.initialize_timing(output_interval, plot_interval, uplift_interval,
report_interval)
def initialize_timing(self, output_interval, plot_interval,
uplift_interval, report_interval):
"""Set up variables related to timing of uplift, output, reporting"""
self.current_time = 0.0
# Next time for output to file
self.next_output = output_interval
# Next time for a plot
if self._show_plots:
self.next_plot = plot_interval
else:
self.next_plot = self.run_duration + 1
# Next time for a progress report to user
self.next_report = report_interval
# Next time to add baselevel adjustment
self.next_uplift = uplift_interval
# Iteration numbers, for output files
self.output_iteration = 1
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=self.settling_rate,
f=self.friction_coef,
motion=self.settling_rate,
swap=self.opt_track_grains,
callback=self.callback_fn)
xn_list = self.add_weathering_and_disturbance_transitions(xn_list,
self.disturbance_rate, self.weathering_rate,
collapse_rate=self.collapse_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self, xn_list, d=0.0, w=0.0,
collapse_rate=0.0,
swap=False, callback=None):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
if d > 0.0:
xn_list.append( Transition((7,0,0), (0,1,0), d, 'disturbance', swap, callback) )
xn_list.append( Transition((7,0,1), (0,2,1), d, 'disturbance', swap, callback) )
xn_list.append( Transition((7,0,2), (0,3,2), d, 'disturbance', swap, callback) )
xn_list.append( Transition((0,7,0), (4,0,0), d, 'disturbance', swap, callback) )
xn_list.append( Transition((0,7,1), (5,0,1), d, 'disturbance', swap, callback) )
xn_list.append( Transition((0,7,2), (6,0,2), d, 'disturbance', swap, callback) )
# Weathering rule
if w > 0.0:
xn_list.append( Transition((8,0,0), (7,0,0), w, 'weathering') )
xn_list.append( Transition((8,0,1), (7,0,1), w, 'weathering') )
xn_list.append( Transition((8,0,2), (7,0,2), w, 'weathering') )
xn_list.append( Transition((0,8,0), (0,7,0), w, 'weathering') )
xn_list.append( Transition((0,8,1), (0,7,1), w, 'weathering') )
xn_list.append( Transition((0,8,2), (0,7,2), w, 'weathering') )
# "Vertical rock collapse" rule: a rock particle overlying air
# will collapse, transitioning to a downward-moving grain
if collapse_rate > 0.0:
xn_list.append( Transition((0,8,0), (4,0,0), collapse_rate,
'rock collapse', swap, callback))
if _DEBUG:
print()
print('setup_transition_list(): list has ' + str(len(xn_list))
+ ' transitions:')
for t in xn_list:
print(' From state ' + str(t.from_state) + ' to state '
+ str(t.to_state) + ' at rate ' + str(t.rate)
+ ' called ' + str(t.name))
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> gh = GrainFacet((5, 7))
>>> gh.grid.at_node['node_state']
array([8, 7, 7, 8, 7, 7, 7, 0, 7, 7, 0, 7, 7, 7, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 2.0:
if (self.grid.node_x[i] > 0.0 and
self.grid.node_x[i] < right_side_x):
nsg[i] = 7
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def run(self, to=None):
"""Run the model."""
if to is None:
run_to = self.run_duration
else:
run_to = to
while self.current_time < run_to:
# Figure out what time to run to this iteration
next_pause = min(self.next_output, self.next_plot)
next_pause = min(next_pause, self.next_uplift)
next_pause = min(next_pause, run_to)
# 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 >= self.next_report:
print('Current sim time' + str(self.current_time) + '(' + \
str(100 * self.current_time / self.run_duration) + '%)')
self.next_report = current_real_time + self.report_interval
# Run until next pause
self.ca.run(next_pause, self.ca.node_state)
self.current_time = next_pause
# Handle output to file
if self.current_time >= self.next_output:
self.write_output(self.grid, 'grain_hill_model',
self.output_iteration)
self.output_iteration += 1
self.next_output += self.output_interval
# Handle plotting on display
if self._show_plots and self.current_time >= self.next_plot:
self.ca_plotter.update_plot()
axis('off')
self.next_plot += self.plot_interval
# Handle uplift
if self.current_time >= self.next_uplift:
self.uplifter.do_offset(
ca=self.ca, current_time=self.current_time,
rock_state=self.rock_state)
self.next_uplift += self.uplift_interval
def get_profile_and_soil_thickness(self, grid, data):
"""Calculate and return profiles of elevation and soil thickness.
Examples
--------
>>> from landlab import HexModelGrid
>>> hg = HexModelGrid(4, 5, shape='rect', orientation='vert')
>>> ns = hg.add_zeros('node', 'node_state', dtype=int)
>>> ns[[0, 3, 1, 6, 4, 9, 2]] = 8
>>> ns[[8, 13, 11, 16, 14]] = 7
>>> gh = GrainHill((3, 7)) # grid size arbitrary here
>>> (elev, thickness) = gh.get_profile_and_soil_thickness(hg, ns)
>>> elev
array([0. , 2.5, 3. , 2.5, 0. ])
>>> thickness
array([0., 2., 2., 1., 0.])
"""
nc = grid.number_of_node_columns
elev = zeros(nc)
soil = zeros(nc)
for col in range(nc):
states = data[grid.nodes[:, col]]
(rows_with_rock_or_sed, ) = where(states > 0)
if len(rows_with_rock_or_sed) == 0:
elev[col] = 0.0
else:
elev[col] = amax(rows_with_rock_or_sed) + 0.5 * (col % 2)
soil[col] = count_nonzero(logical_and(states > 0, states < 8))
return elev, soil
class GrainFacetSimulator(CTSModel):
"""
Model facet-slope evolution with 60-degree normal-fault slip.
"""
def __init__(self,
grid_size,
report_interval=1.0e8,
run_duration=1.0,
output_interval=1.0e99,
disturbance_rate=1.0e-6,
weathering_rate=1.0e-6,
uplift_interval=1.0,
plot_interval=1.0e99,
friction_coef=0.3,
fault_x=1.0,
**kwds):
"""Call the initialize() method."""
self.initialize(grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
uplift_interval, plot_interval, friction_coef, fault_x,
**kwds)
def initialize(self, grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
uplift_interval, plot_interval, friction_coef, fault_x,
**kwds):
"""Initialize the grain hill model."""
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.uplift_interval = uplift_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
# Call base class init
super(GrainFacetSimulator,
self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=True,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
plot_every_transition=False)
ns = self.grid.at_node['node_state']
self.uplifter = LatticeNormalFault(fault_x_intercept=fault_x,
grid=self.grid,
node_state=ns)
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=1.0, f=self.friction_coef)
xn_list = self.add_weathering_and_disturbance_transitions(
xn_list, self.disturbance_rate, self.weathering_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self,
xn_list,
d=0.0,
w=0.0):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
xn_list.append(Transition((7, 0, 0), (0, 1, 0), d, 'disturbance'))
xn_list.append(Transition((7, 0, 1), (0, 2, 1), d, 'disturbance'))
xn_list.append(Transition((7, 0, 2), (0, 3, 2), d, 'disturbance'))
xn_list.append(Transition((0, 7, 0), (4, 0, 0), d, 'disturbance'))
xn_list.append(Transition((0, 7, 1), (5, 0, 1), d, 'disturbance'))
xn_list.append(Transition((0, 7, 2), (6, 0, 2), d, 'disturbance'))
# Weathering rule
xn_list.append(Transition((8, 0, 0), (7, 0, 0), w, 'weathering'))
xn_list.append(Transition((8, 0, 1), (7, 0, 1), w, 'weathering'))
xn_list.append(Transition((8, 0, 2), (7, 0, 2), w, 'weathering'))
xn_list.append(Transition((0, 8, 0), (0, 7, 0), w, 'weathering'))
xn_list.append(Transition((0, 8, 1), (0, 7, 1), w, 'weathering'))
xn_list.append(Transition((0, 8, 2), (0, 7, 2), w, 'weathering'))
if _DEBUG:
print
print 'setup_transition_list(): list has', len(
xn_list), 'transitions:'
for t in xn_list:
print ' From state', t.from_state, 'to state', t.to_state, 'at rate', t.rate, 'called', t.name
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> gh = GrainHill((5, 7))
>>> gh.grid.at_node['node_state']
array([8, 7, 7, 8, 7, 7, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 1.0:
if (self.grid.node_x[i] > 0.0
and self.grid.node_x[i] < right_side_x):
nsg[i] = 7
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def run(self):
"""Run the model."""
# Work out the next times to plot and output
next_output = self.output_interval
next_plot = self.plot_interval
# Next time for a progress report to user
next_report = self.report_interval
# And baselevel adjustment
next_uplift = self.uplift_interval
current_time = 0.0
while current_time < self.run_duration:
# Figure out what time to run to this iteration
next_pause = min(next_output, next_plot)
next_pause = min(next_pause, next_uplift)
next_pause = min(next_pause, self.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' + str(current_time) + '(' + \
str(100 * current_time / self.run_duration) + '%)')
next_report = current_real_time + self.report_interval
# Run the model forward in time until the next output step
print('Running to...' + str(next_pause))
self.ca.run(next_pause, self.ca.node_state) #,
#plot_each_transition=plot_every_transition, plotter=ca_plotter)
current_time = next_pause
# Handle output to file
if current_time >= next_output:
#write_output(hmg, filenm, output_iteration)
#output_iteration += 1
next_output += self.output_interval
# Handle plotting on display
if current_time >= next_plot:
#node_state_grid[hmg.number_of_node_rows-1] = 8
self.ca_plotter.update_plot()
axis('off')
next_plot += self.plot_interval
# Handle fault slip
if current_time >= next_uplift:
self.uplifter.do_offset(rock_state=8)
self.ca.update_link_states_and_transitions(current_time)
next_uplift += self.uplift_interval
def nodes_in_column(self, col, num_rows, num_cols):
"""Return array of node IDs in given column.
Examples
--------
>>> gfs = GrainFacetSimulator((3, 5))
>>> gfs.nodes_in_column(1, 3, 5)
array([ 3, 8, 13])
>>> gfs.nodes_in_column(4, 3, 5)
array([ 2, 7, 12])
>>> gfs = GrainFacetSimulator((3, 6))
>>> gfs.nodes_in_column(3, 3, 6)
array([ 4, 10, 16])
>>> gfs.nodes_in_column(4, 3, 6)
array([ 2, 8, 14])
"""
base_node = (col // 2) + (col % 2) * ((num_cols + 1) // 2)
num_nodes = num_rows * num_cols
return np.arange(base_node, num_nodes, num_cols)
def get_profile_and_soil_thickness(self):
"""Calculate and return the topographic profile and the regolith
thickness."""
nr = self.ca.grid.number_of_node_rows
nc = self.ca.grid.number_of_node_columns
data = self.ca.node_state
elev = np.zeros(nc)
soil = np.zeros(nc)
for c in range(nc):
e = (c % 2) / 2.0
s = 0
r = 0
while r < nr and data[c * nr + r] != 0:
e += 1
if data[c * nr + r] == 7:
s += 1
r += 1
elev[c] = e
soil[c] = s
return elev, soil
class GrainFacetSimulator(CTSModel):
"""
Model facet-slope evolution with 60-degree normal-fault slip.
"""
def __init__(self, grid_size, report_interval=1.0e8, run_duration=1.0,
output_interval=1.0e99, disturbance_rate=0.0,
weathering_rate=0.0, dissolution_rate=0.0,
uplift_interval=1.0, baselevel_rise_interval=0,
plot_interval=1.0e99, friction_coef=0.3,
fault_x=1.0, cell_width=1.0, grav_accel=9.8,
plot_file_name=None, **kwds):
"""Call the initialize() method."""
self.initialize(grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
dissolution_rate, uplift_interval,
baselevel_rise_interval, plot_interval, friction_coef,
fault_x,cell_width, grav_accel, plot_file_name, **kwds)
def initialize(self, grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
dissolution_rate, uplift_interval, baselevel_rise_interval,
plot_interval, friction_coef, fault_x, cell_width,
grav_accel, plot_file_name=None, **kwds):
"""Initialize the grain hill model."""
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.dissolution_rate = dissolution_rate
self.uplift_interval = uplift_interval
self.baselevel_rise_interval = baselevel_rise_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
self.settling_rate = calculate_settling_rate(cell_width, grav_accel)
# Call base class init
super(GrainFacetSimulator, self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=True,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
plot_every_transition=False,
closed_boundaries=(True, True,
False, False))
ns = self.grid.at_node['node_state']
self.uplifter = LatticeNormalFault(fault_x_intercept=fault_x,
grid=self.grid,
node_state=ns)
self.plot_file_name = plot_file_name
if plot_file_name is not None:
self.plot_number = 0
self.plot_to_file()
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=self.settling_rate,
f=self.friction_coef,
motion=self.settling_rate)
xn_list = self.add_weathering_and_disturbance_transitions(xn_list,
self.disturbance_rate, self.weathering_rate,
self.dissolution_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self, xn_list, d=0.0, w=0.0,
diss=0.0):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional, default=0.0)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional, default=0.0)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
diss : float (optional, default=0.0)
Dissolution: rate of transition from fluid / rock pair to
fluid / fluid pair.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
if d > 0.0:
xn_list.append( Transition((7,0,0), (0,1,0), d, 'disturbance') )
xn_list.append( Transition((7,0,1), (0,2,1), d, 'disturbance') )
xn_list.append( Transition((7,0,2), (0,3,2), d, 'disturbance') )
xn_list.append( Transition((0,7,0), (4,0,0), d, 'disturbance') )
xn_list.append( Transition((0,7,1), (5,0,1), d, 'disturbance') )
xn_list.append( Transition((0,7,2), (6,0,2), d, 'disturbance') )
# Weathering rule
if w > 0.0:
xn_list.append( Transition((8,0,0), (7,0,0), w, 'weathering') )
xn_list.append( Transition((8,0,1), (7,0,1), w, 'weathering') )
xn_list.append( Transition((8,0,2), (7,0,2), w, 'weathering') )
xn_list.append( Transition((0,8,0), (0,7,0), w, 'weathering') )
xn_list.append( Transition((0,8,1), (0,7,1), w, 'weathering') )
xn_list.append( Transition((0,8,2), (0,7,2), w, 'weathering') )
# Dissolution rule
if diss > 0.0:
xn_list.append( Transition((8,0,0), (0,0,0), diss, 'dissolution') )
xn_list.append( Transition((8,0,1), (0,0,1), diss, 'dissolution') )
xn_list.append( Transition((8,0,2), (0,0,2), diss, 'dissolution') )
xn_list.append( Transition((0,8,0), (0,0,0), diss, 'dissolution') )
xn_list.append( Transition((0,8,1), (0,0,1), diss, 'dissolution') )
xn_list.append( Transition((0,8,2), (0,0,2), diss, 'dissolution') )
if _DEBUG:
print('')
print('setup_transition_list(): list has ' + str(len(xn_list))
+ ' transitions:')
for t in xn_list:
print(' From state ' + str(t.from_state) + ' to state '
+ str(t.to_state) + ' at rate ' + str(t.rate) + 'called'
+ str(t.name))
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> from grainhill import GrainHill
>>> gh = GrainHill((5, 7))
>>> gh.grid.at_node['node_state'][:20]
array([8, 7, 7, 8, 7, 7, 7, 0, 7, 7, 0, 7, 7, 7, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 2.0:
if (self.grid.node_x[i] > 0.0 and
self.grid.node_x[i] < right_side_x):
nsg[i] = 8
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def run(self):
"""Run the model."""
# Work out the next times to plot and output
next_output = self.output_interval
next_plot = self.plot_interval
# Next time for a progress report to user
next_report = self.report_interval
# And baselevel adjustment
next_uplift = self.uplift_interval
if self.baselevel_rise_interval > 0:
next_baselevel = self.baselevel_rise_interval
baselevel_row = 1
else:
next_baselevel = self.run_duration + 1
current_time = 0.0
while current_time < self.run_duration:
# Figure out what time to run to this iteration
next_pause = min(next_output, next_plot)
next_pause = min(next_pause, next_uplift)
next_pause = min(next_pause, next_baselevel)
next_pause = min(next_pause, self.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' + str(current_time) + '(' + \
str(100 * current_time / self.run_duration) + '%)')
next_report = current_real_time + self.report_interval
# Run the model forward in time until the next output step
print('Running to...' + str(next_pause))
self.ca.run(next_pause, self.ca.node_state)
current_time = next_pause
# Handle output to file
if current_time >= next_output:
next_output += self.output_interval
# Handle plotting on display
if current_time >= next_plot:
self.ca_plotter.update_plot()
if self.plot_file_name is not None:
self.plot_to_file()
next_plot += self.plot_interval
# Handle fault slip
if current_time >= next_uplift:
self.uplifter.do_offset(ca=self.ca, current_time=current_time,
rock_state=8)
for i in range(self.grid.number_of_links):
if self.grid.status_at_link[i] == 4 and self.ca.next_trn_id[i] != -1:
print i
next_uplift += self.uplift_interval
# Handle baselevel rise
if current_time >= next_baselevel:
self.raise_baselevel(baselevel_row)
baselevel_row += 1
next_baselevel += self.baselevel_rise_interval
def raise_baselevel(self, baselevel_row):
"""Raise baselevel on left by closing a node on the left boundary.
Parameters
----------
baselevel_row : int
Row number of the next left-boundary node to be closed
Examples
--------
>>> params = { 'grid_size' : (10,5), 'baselevel_rise_interval' : 1.0 }
>>> params['run_duration'] = 10.0
>>> params['uplift_interval'] = 11.0
>>> gfs = GrainFacetSimulator(**params)
>>> gfs.run()
Current sim time0.0(0.0%)
Running to...1.0
Running to...2.0
Running to...3.0
Running to...4.0
Running to...5.0
Running to...6.0
Running to...7.0
Running to...8.0
Running to...9.0
Running to...10.0
>>> gfs.ca.node_state[:50:5]
array([8, 8, 8, 8, 8, 8, 8, 8, 8, 8])
"""
baselevel_node = self.grid.number_of_node_columns * baselevel_row
if baselevel_node < self.grid.number_of_nodes:
self.ca.node_state[baselevel_node] = 8
self.ca.bnd_lnk[self.grid.links_at_node[baselevel_node]] = True
self.grid.status_at_node[baselevel_node] = CLOSED_BOUNDARY
def nodes_in_column(self, col, num_rows, num_cols):
"""Return array of node IDs in given column.
Examples
--------
>>> gfs = GrainFacetSimulator((3, 5))
>>> gfs.nodes_in_column(1, 3, 5)
array([ 3, 8, 13])
>>> gfs.nodes_in_column(4, 3, 5)
array([ 2, 7, 12])
>>> gfs = GrainFacetSimulator((3, 6))
>>> gfs.nodes_in_column(3, 3, 6)
array([ 4, 10, 16])
>>> gfs.nodes_in_column(4, 3, 6)
array([ 2, 8, 14])
"""
base_node = (col // 2) + (col % 2) * ((num_cols + 1) // 2)
num_nodes = num_rows * num_cols
return np.arange(base_node, num_nodes, num_cols)
def get_profile_and_soil_thickness(self):
"""Calculate and return the topographic profile and the regolith
thickness."""
nr = self.ca.grid.number_of_node_rows
nc = self.ca.grid.number_of_node_columns
data = self.ca.node_state
elev = np.zeros(nc)
soil = np.zeros(nc)
for c in range(nc):
e = (c%2)/2.0
s = 0
r = 0
while r<nr and data[c*nr+r]!=0:
e+=1
if data[c*nr+r]==7:
s+=1
r+=1
elev[c] = e
soil[c] = s
return elev, soil
def report_info_for_debug(self, current_time):
"""Print out various bits of data, for testing and debugging."""
print('\n Current time: ' + str(current_time))
print('Node state:')
print(self.ca.node_state)
for lnk in range(self.grid.number_of_links):
if self.grid.status_at_link[lnk] == 0:
print((lnk, self.grid.node_at_link_tail[lnk],
self.grid.node_at_link_head[lnk],
self.ca.node_state[self.grid.node_at_link_tail[lnk]],
self.ca.node_state[self.grid.node_at_link_head[lnk]],
self.ca.link_state[lnk],self.ca.next_update[lnk],
self.ca.next_trn_id[lnk]))
print('PQ:')
print(self.ca.priority_queue._queue)
def plot_to_file(self):
"""Plot profile of hill to file."""
fname = self.plot_file_name + str(self.plot_number).zfill(4) + '.png'
plot_hill(self.ca.grid, filename=fname)
self.plot_number += 1
class GrainFacetSimulator(CTSModel):
"""
Model facet-slope evolution with 60-degree normal-fault slip.
"""
def __init__(self,
grid_size,
report_interval=1.0e8,
run_duration=1.0,
output_interval=1.0e99,
disturbance_rate=0.0,
weathering_rate=0.0,
dissolution_rate=0.0,
uplift_interval=1.0,
plot_interval=1.0e99,
friction_coef=0.3,
fault_x=1.0,
cell_width=1.0,
grav_accel=9.8,
plot_file_name=None,
**kwds):
"""Call the initialize() method."""
self.initialize(grid_size, report_interval, run_duration,
output_interval, disturbance_rate, weathering_rate,
dissolution_rate, uplift_interval, plot_interval,
friction_coef, fault_x, cell_width, grav_accel,
plot_file_name, **kwds)
def initialize(self,
grid_size,
report_interval,
run_duration,
output_interval,
disturbance_rate,
weathering_rate,
dissolution_rate,
uplift_interval,
plot_interval,
friction_coef,
fault_x,
cell_width,
grav_accel,
plot_file_name=None,
**kwds):
"""Initialize the grain hill model."""
self.disturbance_rate = disturbance_rate
self.weathering_rate = weathering_rate
self.dissolution_rate = dissolution_rate
self.uplift_interval = uplift_interval
self.plot_interval = plot_interval
self.friction_coef = friction_coef
self.settling_rate = calculate_settling_rate(cell_width, grav_accel)
# Call base class init
super(GrainFacetSimulator,
self).initialize(grid_size=grid_size,
report_interval=report_interval,
grid_orientation='vertical',
grid_shape='rect',
show_plots=True,
cts_type='oriented_hex',
run_duration=run_duration,
output_interval=output_interval,
plot_every_transition=False)
# Close top and right edges so as to avoid boundary bug issue
for edge in (self.grid.nodes_at_right_edge,
self.grid.nodes_at_top_edge):
self.grid.status_at_node[edge] = CLOSED_BOUNDARY
ns = self.grid.at_node['node_state']
self.uplifter = LatticeNormalFault(fault_x_intercept=fault_x,
grid=self.grid,
node_state=ns)
self.plot_file_name = plot_file_name
if plot_file_name is not None:
self.plot_number = 0
self.plot_to_file()
def node_state_dictionary(self):
"""
Create and return dict of node states.
Overrides base-class method. Here, we simply call on a function in
the lattice_grain module.
"""
return lattice_grain_node_states()
def transition_list(self):
"""
Make and return list of Transition object.
"""
xn_list = lattice_grain_transition_list(g=self.settling_rate,
f=self.friction_coef,
motion=self.settling_rate)
xn_list = self.add_weathering_and_disturbance_transitions(
xn_list, self.disturbance_rate, self.weathering_rate,
self.dissolution_rate)
return xn_list
def add_weathering_and_disturbance_transitions(self,
xn_list,
d=0.0,
w=0.0,
diss=0.0):
"""
Add transition rules representing weathering and/or grain disturbance
to the list, and return the list.
Parameters
----------
xn_list : list of Transition objects
List of objects that encode information about the link-state
transitions. Normally should first be initialized with lattice-grain
transition rules, then passed to this function to add rules for
weathering and disturbance.
d : float (optional, default=0.0)
Rate of transition (1/time) from fluid / resting grain pair to
mobile-grain / fluid pair, representing grain disturbance.
w : float (optional, default=0.0)
Rate of transition (1/time) from fluid / rock pair to
fluid / resting-grain pair, representing weathering.
diss : float (optional, default=0.0)
Dissolution: rate of transition from fluid / rock pair to
fluid / fluid pair.
Returns
-------
xn_list : list of Transition objects
Modified transition list.
"""
# Disturbance rule
if d > 0.0:
xn_list.append(Transition((7, 0, 0), (0, 1, 0), d, 'disturbance'))
xn_list.append(Transition((7, 0, 1), (0, 2, 1), d, 'disturbance'))
xn_list.append(Transition((7, 0, 2), (0, 3, 2), d, 'disturbance'))
xn_list.append(Transition((0, 7, 0), (4, 0, 0), d, 'disturbance'))
xn_list.append(Transition((0, 7, 1), (5, 0, 1), d, 'disturbance'))
xn_list.append(Transition((0, 7, 2), (6, 0, 2), d, 'disturbance'))
# Weathering rule
if w > 0.0:
xn_list.append(Transition((8, 0, 0), (7, 0, 0), w, 'weathering'))
xn_list.append(Transition((8, 0, 1), (7, 0, 1), w, 'weathering'))
xn_list.append(Transition((8, 0, 2), (7, 0, 2), w, 'weathering'))
xn_list.append(Transition((0, 8, 0), (0, 7, 0), w, 'weathering'))
xn_list.append(Transition((0, 8, 1), (0, 7, 1), w, 'weathering'))
xn_list.append(Transition((0, 8, 2), (0, 7, 2), w, 'weathering'))
# Dissolution rule
if diss > 0.0:
xn_list.append(
Transition((8, 0, 0), (0, 0, 0), diss, 'dissolution'))
xn_list.append(
Transition((8, 0, 1), (0, 0, 1), diss, 'dissolution'))
xn_list.append(
Transition((8, 0, 2), (0, 0, 2), diss, 'dissolution'))
xn_list.append(
Transition((0, 8, 0), (0, 0, 0), diss, 'dissolution'))
xn_list.append(
Transition((0, 8, 1), (0, 0, 1), diss, 'dissolution'))
xn_list.append(
Transition((0, 8, 2), (0, 0, 2), diss, 'dissolution'))
if _DEBUG:
print('')
print('setup_transition_list(): list has ' + str(len(xn_list)) +
' transitions:')
for t in xn_list:
print(' From state ' + str(t.from_state) + ' to state ' +
str(t.to_state) + ' at rate ' + str(t.rate) + 'called' +
str(t.name))
return xn_list
def initialize_node_state_grid(self):
"""Set up initial node states.
Examples
--------
>>> from grainhill import GrainHill
>>> gh = GrainHill((5, 7))
>>> gh.grid.at_node['node_state']
array([8, 7, 7, 8, 7, 7, 7, 0, 7, 7, 0, 7, 7, 7, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
"""
# For shorthand, get a reference to the node-state grid
nsg = self.grid.at_node['node_state']
# Fill the bottom two rows with grains
right_side_x = 0.866025403784 * (self.grid.number_of_node_columns - 1)
for i in range(self.grid.number_of_nodes):
if self.grid.node_y[i] < 2.0:
if (self.grid.node_x[i] > 0.0
and self.grid.node_x[i] < right_side_x):
nsg[i] = 8
# Place "wall" particles in the lower-left and lower-right corners
if self.grid.number_of_node_columns % 2 == 0:
bottom_right = self.grid.number_of_node_columns - 1
else:
bottom_right = self.grid.number_of_node_columns // 2
nsg[0] = 8 # bottom left
nsg[bottom_right] = 8
return nsg
def run(self):
"""Run the model."""
# Work out the next times to plot and output
next_output = self.output_interval
next_plot = self.plot_interval
# Next time for a progress report to user
next_report = self.report_interval
# And baselevel adjustment
next_uplift = self.uplift_interval
current_time = 0.0
while current_time < self.run_duration:
# Figure out what time to run to this iteration
next_pause = min(next_output, next_plot)
next_pause = min(next_pause, next_uplift)
next_pause = min(next_pause, self.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' + str(current_time) + '(' + \
str(100 * current_time / self.run_duration) + '%)')
next_report = current_real_time + self.report_interval
# Run the model forward in time until the next output step
print('Running to...' + str(next_pause))
self.ca.run(next_pause, self.ca.node_state)
current_time = next_pause
# Handle output to file
if current_time >= next_output:
next_output += self.output_interval
# Handle plotting on display
if current_time >= next_plot:
self.ca_plotter.update_plot()
if self.plot_file_name is not None:
self.plot_to_file()
next_plot += self.plot_interval
# Handle fault slip
if current_time >= next_uplift:
self.uplifter.do_offset(ca=self.ca,
current_time=current_time,
rock_state=8)
next_uplift += self.uplift_interval
def nodes_in_column(self, col, num_rows, num_cols):
"""Return array of node IDs in given column.
Examples
--------
>>> gfs = GrainFacetSimulator((3, 5))
>>> gfs.nodes_in_column(1, 3, 5)
array([ 3, 8, 13])
>>> gfs.nodes_in_column(4, 3, 5)
array([ 2, 7, 12])
>>> gfs = GrainFacetSimulator((3, 6))
>>> gfs.nodes_in_column(3, 3, 6)
array([ 4, 10, 16])
>>> gfs.nodes_in_column(4, 3, 6)
array([ 2, 8, 14])
"""
base_node = (col // 2) + (col % 2) * ((num_cols + 1) // 2)
num_nodes = num_rows * num_cols
return np.arange(base_node, num_nodes, num_cols)
def get_profile_and_soil_thickness(self):
"""Calculate and return the topographic profile and the regolith
thickness."""
nr = self.ca.grid.number_of_node_rows
nc = self.ca.grid.number_of_node_columns
data = self.ca.node_state
elev = np.zeros(nc)
soil = np.zeros(nc)
for c in range(nc):
e = (c % 2) / 2.0
s = 0
r = 0
while r < nr and data[c * nr + r] != 0:
e += 1
if data[c * nr + r] == 7:
s += 1
r += 1
elev[c] = e
soil[c] = s
return elev, soil
def report_info_for_debug(self, current_time):
"""Print out various bits of data, for testing and debugging."""
print('\n Current time: ' + str(current_time))
print('Node state:')
print(self.ca.node_state)
for lnk in range(self.grid.number_of_links):
if self.grid.status_at_link[lnk] == 0:
print((lnk, self.grid.node_at_link_tail[lnk],
self.grid.node_at_link_head[lnk],
self.ca.node_state[self.grid.node_at_link_tail[lnk]],
self.ca.node_state[self.grid.node_at_link_head[lnk]],
self.ca.link_state[lnk], self.ca.next_update[lnk],
self.ca.next_trn_id[lnk]))
print('PQ:')
print(self.ca.priority_queue._queue)
def plot_to_file(self):
"""Plot profile of hill to file."""
fname = self.plot_file_name + str(self.plot_number).zfill(4) + '.png'
plot_hill(self.ca.grid, filename=fname)
self.plot_number += 1