<commit_before>#! /usr/env/python
"""

Component that models 2D diffusion using an explicit finite-volume method.

Created July 2013 GT
Last updated May 2015 DEJH

"""

##############DEJH is unsure if the uplift is correctly (not) incorporated here


from __future__ import print_function

from landlab import ModelParameterDictionary, Component, FieldError
from landlab import create_and_initialize_grid
from landlab.core.model_parameter_dictionary import MissingKeyError

_ALPHA = 0.25   # time-step stability factor

#_VERSION = 'make_all_data'
#_VERSION = 'explicit'
_VERSION = 'pass_grid'


class LinearDiffuser(Component):
    """
    This component implements linear diffusion of a field in the supplied
    ModelGrid.

    This components requires the following parameters be set in the input file,
    *input_stream*, set in the component initialization:

        'linear_diffusivity', the diffusivity to use

    Optional inputs are:

        'uplift_rate', if you want this component to include the uplift
            internally
        'dt', the model timestep (assumed constant)
        'values_to_diffuse', a string giving the name of the grid field
        containing the data to diffuse.

    Supply *dt* to the diffuser through the diffuse() argument.
    This allows you to set a dynamic timestep for this class.
    If 'values_to_diffuse' is not provided, defaults to
    'topographic__elevation'.

    No particular units are necessary where they are not specified, as long as
    all units are internally consistent.

    The component takes *grid*, the ModelGrid object, and (optionally)
    *current_time* and *input_stream*. If *current_time* is not set, it defaults
    to 0.0. If *input_stream* is not set in instantiation of the class,
    :func:`initialize` with *input_stream* as in input must be called instead.
    *Input_stream* is the filename of (& optionally, path to) the parameter
    file.

    At the moment, this diffuser can only work with constant diffusivity.
    Spatially variable diffusivity hopefully coming soon.

    The primary method of this class is :func:`diffuse`.
    """

    _name = 'LinearDiffuser'

    _input_var_names = set(['topographic__elevation',
                            ])

#############################UPDATE ME
    _output_var_names = set(['topographic__elevation',
                             'surface_gradient',
                             'unit_flux',
                             ])

    _var_units = {'topographic__elevation' : 'm',
                  'surface_gradient' : '-',
                  'unit_flux' : 'm**3/s',
                  }

    _var_mapping = {'topographic__elevation' : 'node',
                    'surface_gradient' : 'link',
                    'unit_flux' : 'link',
                    }

    _var_defs = {'topographic__elevation' : 'Land surface topographic elevation; can be overwritten in initialization',
                 'surface_gradient' : 'Gradient of surface, on links',
                 'unit_flux' : 'Volume flux per unit width along links',
                  }

    def __init__(self, grid, input_stream=None, current_time=0.):
        self._grid = grid
        self.current_time = current_time
        if input_stream:
            self.initialize(input_stream)
        else:
            print('Ensure you call the initialize(input_stream) method before '
                  'running the model!')

    def initialize(self, input_stream):

        # Create a ModelParameterDictionary for the inputs
        if type(input_stream)==ModelParameterDictionary:
            inputs = input_stream
        else:
            inputs = ModelParameterDictionary(input_stream)

        # Read input/configuration parameters
        self.kd = inputs.read_float('linear_diffusivity')
        try:
            self.uplift_rate = inputs.read_float('uplift_rate')
        except MissingKeyError:
            self.uplift_rate = 0.
        try:
            self.values_to_diffuse = inputs.read_string('values_to_diffuse')
        except MissingKeyError:
            self.values_to_diffuse = 'topographic__elevation'
        else:
            #take switch in the new field name in the class properties
            for mysets in (self._input_var_names, self._output_var_names):
                mysets.remove('topographic__elevation')
                mysets.add(self.values_to_diffuse)
            for mydicts in (self._var_units, self._var_mapping, self._var_defs):
                mydicts[self.values_to_diffuse] = mydicts.pop('topographic__elevation')

        try:
            self.timestep_in = inputs.read_float('dt')
        except MissingKeyError:
            pass


        # Create grid if one doesn't already exist
        if self._grid is None:
            self._grid = create_and_initialize_grid(input_stream)

        # Set internal time step
        # ..todo:
        #   implement mechanism to compute time-steps dynamically if grid is
        #   adaptive/changing
        dx = self._grid.min_active_link_length()  # smallest active link length
        self.dt = _ALPHA*dx*dx/self.kd  # CFL condition
        try:
            self.tstep_ratio = self.timestep_in/self.dt
        except AttributeError:
            pass

        # Get a list of interior cells
        self.interior_cells = self._grid.get_core_cell_node_ids()

##DEJH bites the bullet and forces the 2015 style with fields
#        # Here we're experimenting with different approaches: with
#        # 'make_all_data', we create and manage all the data we need and embed
#        # it all in the grid. With 'explicit', we require the caller/user to
#        # provide data.
#        if _VERSION=='make_all_data':
#            #print('creating internal data')
#            self.z = self._grid.add_zeros('node', 'landscape_surface__elevation')
#            self.g = self._grid.add_zeros('active_link', 'landscape_surface__gradient')  # surface gradients
#            self.qs = self._grid.add_zeros('active_link','unit_sediment_flux')  # unit sediment flux
#            self.dqds = self._grid.add_zeros('node', 'sediment_flux_divergence')  # sed flux derivative
#        elif _VERSION=='explicit':
#            pass
#        else:
#            # Create data arrays for variables that won't (?) be shared with other
#            # components
#            self.g = self._grid.create_active_link_array_zeros()  # surface gradients
#            self.qs = self._grid.create_active_link_array_zeros()  # unit sediment flux
#            self.dqds = self._grid.create_node_array_zeros()  # sed flux derivative

        self.z = self._grid.at_node[self.values_to_diffuse]
        g = self._grid.zeros(centering='link')
        qs = self._grid.zeros(centering='link')
        try:
            self.g = self._grid.add_field('link', 'surface__gradient', g, noclobber=True) #note this will object if this exists already
        except FieldError:
            pass #field exists, so no problem
        try:
            self.qs = self._grid.add_field('link', 'unit_flux', qs, noclobber=True)
        except FieldError:
            pass
        #note all these terms are deliberately loose, as we won't always be dealing with topo


    def input_timestep(self, timestep_in):
        """
        Allows the user to set a dynamic (evolving) timestep manually as part of
        a run loop.
        """
        self.timestep_in = timestep_in
        self.tstep_ratio = timestep_in/self.dt


    def run_one_step_explicit(self, mg, z, g, qs, dqsds, dzdt, delt):

        # Take the smaller of delt or built-in time-step size self.dt
        dt = min(self.dt, delt)

        # Calculate the gradients and sediment fluxes
        g = mg.calculate_gradients_at_active_links(z)
        qs = -self.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 = self.uplift_rate - dqsds

        # Update the elevations
        z[self.interior_cells] = z[self.interior_cells] \
                                 + dzdt[self.interior_cells] * dt

        # Update current time and return it
        self.current_time += dt

        return z, g, qs, dqsds, dzdt


    def run_one_step_internal(self, delt):

        # Take the smaller of delt or built-in time-step size self.dt
        dt = min(self.dt, delt)

        # Calculate the gradients and sediment fluxes
        self.g = self._grid.calculate_gradients_at_active_links(self.z)
        self.qs = -self.kd*self.g

        # Calculate the net deposition/erosion rate at each node
        self.dqsds = self._grid.calculate_flux_divergence_at_nodes(self.qs)

        # Calculate the total rate of elevation change
        dzdt = self.uplift_rate - self.dqsds

        # Update the elevations
        self.z[self.interior_cells] += dzdt[self.interior_cells] * dt

        # Update current time and return it
        self.current_time += dt
        return self.current_time

    def diffuse(self, dt, internal_uplift=False, num_uplift_implicit_comps = 1):
        """
        This is the primary method of the class. Call it to perform an iteration
        of the model. Takes *dt*, the current timestep.

        The modelgrid must contain the field to diffuse, which defaults to
        'topographic__elevation'. This can be overridden with the
        values_to_diffuse property in the input file.

        See the class docstring for a list of the other properties necessary
        in the input file for this component to run.

        To improve stability, this component can incorporate uplift into its
        internal mechanism. To use this, set *internal_uplift* to True, and . If you only have one module that requires this, do not add
        uplift manually in your loop; this method will include uplift
        automatically. If more than one of your components has this requirement,
        set *num_uplift_implicit_comps* to the total number of components that
        do.

        You can suppress this behaviour by setting *internal_uplift* to False.

        """
        # Take the smaller of delt or built-in time-step size self.dt
        self.tstep_ratio = dt/self.dt
        repeats = int(self.tstep_ratio//1.)
        extra_time = self.tstep_ratio-repeats
        z = self._grid.at_node[self.values_to_diffuse]

        core_nodes = self._grid.get_core_cell_node_ids()

        for i in xrange(repeats+1):
            print(repeats, extra_time)
            # Calculate the gradients and sediment fluxes
            self.g[self._grid.active_links] = self._grid.calculate_gradients_at_active_links(z)
            self.qs[self._grid.active_links] = -self.kd*self.g[self._grid.active_links]

            # Calculate the net deposition/erosion rate at each node
            self.dqsds = self._grid.calculate_flux_divergence_at_nodes(self.qs[self._grid.active_links])

            # Calculate the total rate of elevation change
            #dzdt = self.uplift_rate - self.dqsds
            dzdt = - self.dqsds

            # Update the elevations
            timestep = self.dt
            if i == (repeats):
                timestep *= extra_time
            else:
                pass
            if internal_uplift:
                add_uplift = self.uplift_rate/num_uplift_implicit_comps
            else:
                add_uplift = 0.
            self._grid.at_node[self.values_to_diffuse][core_nodes] += add_uplift + dzdt[core_nodes] * timestep
            print(timestep)

            #check the BCs, update if fixed gradient
            if self._grid.fixed_gradient_boundary_nodes:
                self._grid.at_node[self.values_to_diffuse][self._grid.fixed_gradient_node_properties['boundary_node_IDs']] = self._grid.at_node[self.values_to_diffuse][self._grid.fixed_gradient_node_properties['anchor_node_IDs']] + self._grid.fixed_gradient_node_properties['values_to_add']

        #return the grid
        return self._grid


    def run_until_explicit(self, mg, t, z, g, qs, dqsds, dzdt):

        while self.current_time < t:
            remaining_time = t - self.current_time
            z, g, qs, dqsds, dzdt = self.run_one_step_explicit(mg, z, g, qs, dqsds, dzdt, remaining_time)

        return z, g, qs, dqsds, dzdt
<commit_msg>remove print statements<commit_after>#! /usr/env/python
"""

Component that models 2D diffusion using an explicit finite-volume method.

Created July 2013 GT
Last updated May 2015 DEJH

"""

##############DEJH is unsure if the uplift is correctly (not) incorporated here


from __future__ import print_function

from landlab import ModelParameterDictionary, Component, FieldError
from landlab import create_and_initialize_grid
from landlab.core.model_parameter_dictionary import MissingKeyError

_ALPHA = 0.25   # time-step stability factor

#_VERSION = 'make_all_data'
#_VERSION = 'explicit'
_VERSION = 'pass_grid'


class LinearDiffuser(Component):
    """
    This component implements linear diffusion of a field in the supplied
    ModelGrid.

    This components requires the following parameters be set in the input file,
    *input_stream*, set in the component initialization:

        'linear_diffusivity', the diffusivity to use

    Optional inputs are:

        'uplift_rate', if you want this component to include the uplift
            internally
        'dt', the model timestep (assumed constant)
        'values_to_diffuse', a string giving the name of the grid field
        containing the data to diffuse.

    Supply *dt* to the diffuser through the diffuse() argument.
    This allows you to set a dynamic timestep for this class.
    If 'values_to_diffuse' is not provided, defaults to
    'topographic__elevation'.

    No particular units are necessary where they are not specified, as long as
    all units are internally consistent.

    The component takes *grid*, the ModelGrid object, and (optionally)
    *current_time* and *input_stream*. If *current_time* is not set, it defaults
    to 0.0. If *input_stream* is not set in instantiation of the class,
    :func:`initialize` with *input_stream* as in input must be called instead.
    *Input_stream* is the filename of (& optionally, path to) the parameter
    file.

    At the moment, this diffuser can only work with constant diffusivity.
    Spatially variable diffusivity hopefully coming soon.

    The primary method of this class is :func:`diffuse`.
    """

    _name = 'LinearDiffuser'

    _input_var_names = set(['topographic__elevation',
                            ])

#############################UPDATE ME
    _output_var_names = set(['topographic__elevation',
                             'surface_gradient',
                             'unit_flux',
                             ])

    _var_units = {'topographic__elevation' : 'm',
                  'surface_gradient' : '-',
                  'unit_flux' : 'm**3/s',
                  }

    _var_mapping = {'topographic__elevation' : 'node',
                    'surface_gradient' : 'link',
                    'unit_flux' : 'link',
                    }

    _var_defs = {'topographic__elevation' : 'Land surface topographic elevation; can be overwritten in initialization',
                 'surface_gradient' : 'Gradient of surface, on links',
                 'unit_flux' : 'Volume flux per unit width along links',
                  }

    def __init__(self, grid, input_stream=None, current_time=0.):
        self._grid = grid
        self.current_time = current_time
        if input_stream:
            self.initialize(input_stream)
        else:
            print('Ensure you call the initialize(input_stream) method before '
                  'running the model!')

    def initialize(self, input_stream):

        # Create a ModelParameterDictionary for the inputs
        if type(input_stream)==ModelParameterDictionary:
            inputs = input_stream
        else:
            inputs = ModelParameterDictionary(input_stream)

        # Read input/configuration parameters
        self.kd = inputs.read_float('linear_diffusivity')
        try:
            self.uplift_rate = inputs.read_float('uplift_rate')
        except MissingKeyError:
            self.uplift_rate = 0.
        try:
            self.values_to_diffuse = inputs.read_string('values_to_diffuse')
        except MissingKeyError:
            self.values_to_diffuse = 'topographic__elevation'
        else:
            #take switch in the new field name in the class properties
            for mysets in (self._input_var_names, self._output_var_names):
                mysets.remove('topographic__elevation')
                mysets.add(self.values_to_diffuse)
            for mydicts in (self._var_units, self._var_mapping, self._var_defs):
                mydicts[self.values_to_diffuse] = mydicts.pop('topographic__elevation')

        try:
            self.timestep_in = inputs.read_float('dt')
        except MissingKeyError:
            pass


        # Create grid if one doesn't already exist
        if self._grid is None:
            self._grid = create_and_initialize_grid(input_stream)

        # Set internal time step
        # ..todo:
        #   implement mechanism to compute time-steps dynamically if grid is
        #   adaptive/changing
        dx = self._grid.min_active_link_length()  # smallest active link length
        self.dt = _ALPHA*dx*dx/self.kd  # CFL condition
        try:
            self.tstep_ratio = self.timestep_in/self.dt
        except AttributeError:
            pass

        # Get a list of interior cells
        self.interior_cells = self._grid.get_core_cell_node_ids()

##DEJH bites the bullet and forces the 2015 style with fields
#        # Here we're experimenting with different approaches: with
#        # 'make_all_data', we create and manage all the data we need and embed
#        # it all in the grid. With 'explicit', we require the caller/user to
#        # provide data.
#        if _VERSION=='make_all_data':
#            #print('creating internal data')
#            self.z = self._grid.add_zeros('node', 'landscape_surface__elevation')
#            self.g = self._grid.add_zeros('active_link', 'landscape_surface__gradient')  # surface gradients
#            self.qs = self._grid.add_zeros('active_link','unit_sediment_flux')  # unit sediment flux
#            self.dqds = self._grid.add_zeros('node', 'sediment_flux_divergence')  # sed flux derivative
#        elif _VERSION=='explicit':
#            pass
#        else:
#            # Create data arrays for variables that won't (?) be shared with other
#            # components
#            self.g = self._grid.create_active_link_array_zeros()  # surface gradients
#            self.qs = self._grid.create_active_link_array_zeros()  # unit sediment flux
#            self.dqds = self._grid.create_node_array_zeros()  # sed flux derivative

        self.z = self._grid.at_node[self.values_to_diffuse]
        g = self._grid.zeros(centering='link')
        qs = self._grid.zeros(centering='link')
        try:
            self.g = self._grid.add_field('link', 'surface__gradient', g, noclobber=True) #note this will object if this exists already
        except FieldError:
            pass #field exists, so no problem
        try:
            self.qs = self._grid.add_field('link', 'unit_flux', qs, noclobber=True)
        except FieldError:
            pass
        #note all these terms are deliberately loose, as we won't always be dealing with topo


    def input_timestep(self, timestep_in):
        """
        Allows the user to set a dynamic (evolving) timestep manually as part of
        a run loop.
        """
        self.timestep_in = timestep_in
        self.tstep_ratio = timestep_in/self.dt


    def run_one_step_explicit(self, mg, z, g, qs, dqsds, dzdt, delt):

        # Take the smaller of delt or built-in time-step size self.dt
        dt = min(self.dt, delt)

        # Calculate the gradients and sediment fluxes
        g = mg.calculate_gradients_at_active_links(z)
        qs = -self.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 = self.uplift_rate - dqsds

        # Update the elevations
        z[self.interior_cells] = z[self.interior_cells] \
                                 + dzdt[self.interior_cells] * dt

        # Update current time and return it
        self.current_time += dt

        return z, g, qs, dqsds, dzdt


    def run_one_step_internal(self, delt):

        # Take the smaller of delt or built-in time-step size self.dt
        dt = min(self.dt, delt)

        # Calculate the gradients and sediment fluxes
        self.g = self._grid.calculate_gradients_at_active_links(self.z)
        self.qs = -self.kd*self.g

        # Calculate the net deposition/erosion rate at each node
        self.dqsds = self._grid.calculate_flux_divergence_at_nodes(self.qs)

        # Calculate the total rate of elevation change
        dzdt = self.uplift_rate - self.dqsds

        # Update the elevations
        self.z[self.interior_cells] += dzdt[self.interior_cells] * dt

        # Update current time and return it
        self.current_time += dt
        return self.current_time

    def diffuse(self, dt, internal_uplift=False, num_uplift_implicit_comps = 1):
        """
        This is the primary method of the class. Call it to perform an iteration
        of the model. Takes *dt*, the current timestep.

        The modelgrid must contain the field to diffuse, which defaults to
        'topographic__elevation'. This can be overridden with the
        values_to_diffuse property in the input file.

        See the class docstring for a list of the other properties necessary
        in the input file for this component to run.

        To improve stability, this component can incorporate uplift into its
        internal mechanism. To use this, set *internal_uplift* to True, and . If you only have one module that requires this, do not add
        uplift manually in your loop; this method will include uplift
        automatically. If more than one of your components has this requirement,
        set *num_uplift_implicit_comps* to the total number of components that
        do.

        You can suppress this behaviour by setting *internal_uplift* to False.

        """
        # Take the smaller of delt or built-in time-step size self.dt
        self.tstep_ratio = dt/self.dt
        repeats = int(self.tstep_ratio//1.)
        extra_time = self.tstep_ratio-repeats
        z = self._grid.at_node[self.values_to_diffuse]

        core_nodes = self._grid.get_core_cell_node_ids()

        for i in xrange(repeats+1):
            # Calculate the gradients and sediment fluxes
            self.g[self._grid.active_links] = self._grid.calculate_gradients_at_active_links(z)
            self.qs[self._grid.active_links] = -self.kd*self.g[self._grid.active_links]

            # Calculate the net deposition/erosion rate at each node
            self.dqsds = self._grid.calculate_flux_divergence_at_nodes(self.qs[self._grid.active_links])

            # Calculate the total rate of elevation change
            #dzdt = self.uplift_rate - self.dqsds
            dzdt = - self.dqsds

            # Update the elevations
            timestep = self.dt
            if i == (repeats):
                timestep *= extra_time
            else:
                pass
            if internal_uplift:
                add_uplift = self.uplift_rate/num_uplift_implicit_comps
            else:
                add_uplift = 0.
            self._grid.at_node[self.values_to_diffuse][core_nodes] += add_uplift + dzdt[core_nodes] * timestep

            #check the BCs, update if fixed gradient
            if self._grid.fixed_gradient_boundary_nodes:
                self._grid.at_node[self.values_to_diffuse][self._grid.fixed_gradient_node_properties['boundary_node_IDs']] = self._grid.at_node[self.values_to_diffuse][self._grid.fixed_gradient_node_properties['anchor_node_IDs']] + self._grid.fixed_gradient_node_properties['values_to_add']

        #return the grid
        return self._grid


    def run_until_explicit(self, mg, t, z, g, qs, dqsds, dzdt):

        while self.current_time < t:
            remaining_time = t - self.current_time
            z, g, qs, dqsds, dzdt = self.run_one_step_explicit(mg, z, g, qs, dqsds, dzdt, remaining_time)

        return z, g, qs, dqsds, dzdt

{'fraction_non_alphanumeric': 0.07964601769911504, 'fraction_numerical': 0.0020390685534847682, 'mean_word_length': 2.403942254303165, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3004677', 'n_tokens_mistral': 7283, 'n_tokens_neox': 6884, 'n_words': 2065}