Exemple #1
0
def prepare_inputs_for_forward_model(k):
    ''' make directory to run the fowrard model in, copy across the input files and
        modify the time step in flml so the forward model will run just for one time step'''             
    # make a directory to run the code in and copy across input files
    cwd = os.getcwd()
    input_file_name = "fwd_model.flml" 
#             print "files in cwd"
#             for files in os.listdir(cwd):
#                print files
    if not os.path.isdir( str(k) ):
        print "attempting to mkdir" 
        os.mkdir(str(k))
        os.system('cp *.msh ' + str(k))
        os.system('cp *_' +str(k)+ '_checkpoint* ' + str(k))

        os.chdir(str(k))

        # modify the checkpoint file times
        for files in os.listdir('./'):
            # get the name of the checkpoint flml     
            if files.endswith(str(k)+"_checkpoint.flml"):
#               pos = files.rfind('.')
                checkpoint_file_name = files
#               print "checkpoint fname", checkpoint_file_name

                # load options from checkpoint file
                libspud.load_options(checkpoint_file_name)

                # change the name of the output 
                libspud.set_option('/simulation_name','2d_canyon')

                # change the final time so it runs from t_k to t_k+1 only
                t0 = libspud.get_option('/timestepping/current_time')
                dt = libspud.get_option('/timestepping/timestep')
                libspud.set_option('/timestepping/finish_time',t0+dt)
                # could check with vtu's that these are the correct times

                # rename input file
                libspud.write_options(input_file_name)
                libspud.clear_options()

    os.chdir(cwd)

    return input_file_name
try:
    libspud.add_option('/foo')
except libspud.SpudNewKeyWarning, e:
    print "caught libspud.SpudNewKeyWarning: " + e.message
print libspud.option_count('/foo')

libspud.set_option('/problem_type', 'helloworld')
print libspud.get_option('/problem_type')

try:
    libspud.set_option_attribute('/foo/bar', 'foobar')
except libspud.SpudNewKeyWarning, e:
    print "caught libspud.SpudNewKeyWarning: " + e.message
print libspud.get_option('/foo/bar')

libspud.delete_option('/foo')
print libspud.option_count('/foo')

try:
    libspud.get_option('/foo')
except libspud.SpudKeyError, e:
    print "caught libspud.SpudKeyError: " + e.message

try:
    libspud.get_option('/geometry')
except libspud.SpudTypeError, e:
    print "caught libspud.SpudTypeError: " + e.message

libspud.write_options('test_out.flml')
Exemple #3
0
def data_assimilation(opal_options):

   global Model_updated, iter_count

   # functions used within data_assimilation: J() and gradJ()
   def J(v):
	global Model_updated, iter_count

        iter_count = iter_count + 1

        vT = np.transpose(v)
        vTv = np.dot(vT,v)
        Vv = np.dot(V,v)
        HVv = np.dot(H,Vv)

        # we need the model results - check if these are already available, if not, run the forward model with Vv as the input
        if Model_updated:
             print "in J(): using pre-exiting forward model model solution"
             Model_updated = False
        else:
             print "in J(): updating the forward model solution"

             # prepare directory and input files for forward model
             input_file_name = prepare_inputs_for_forward_model(k)

             # modify initial condition of tracer
             field = modify_initial_conditions_at_tk(k,Vv)

             # run forward model
             run_forward_model_tk(k,opal_options.executable,input_file_name)

             Model_updated = True

        # retrieve the forward model results, MVv
        path_to_vtu_file = str(k) + '/2d_canyon_1.vtu'
        vtu_data = vtktools.vtu(path_to_vtu_file)
        MVv = vtu_data.GetScalarField(field)
#        print "J(): MVv[0:10]", MVv[0:10]

        ##MVv = np.dot(M,Vv)
        HMVv = np.dot(H,MVv)
        Jmis = np.subtract(HVv,d)
        JmisM = np.subtract(HMVv,d)
        invR = np.linalg.inv(R)
        JmisT = np.transpose(Jmis)
        JmisMT = np.transpose(JmisM)
        RJmis = np.dot(invR,JmisT)
        RJmisM = np.dot(invR,JmisMT)
        J1 = np.dot(Jmis,RJmis)
        JM1 = np.dot(JmisM,RJmisM)

        Jv = (vTv + J1 + JM1) / 2

        return Jv    
    
###############################################
#######         GRADIENT OF J          ########
###############################################


   def gradJ(v):
        global Model_updated

        Vv = np.dot(V,v)
        HVv = np.dot(H,Vv)

        # CODE COPIED FROM J() ###########################################
        # we need the model results - check if these are already available, 
        # if not, run the forward model with Vv as the input
        if Model_updated:
             print "in gradJ(): using pre-exiting forward model model solution"
             Model_updated = False
        else:
             print "in gradJ(): updating the forward model solution"

             # prepare directory and input files for forward model
             input_file_name = prepare_inputs_for_forward_model(k)

             # modify initial condition of tracer
             field = modify_initial_conditions_at_tk(k,Vv)

             # run forward model
             run_forward_model_tk(k,opal_options.executable,input_file_name)

             Model_updated = True

        # END OF CODE COPIED FROM J() ###########################################

        # MVv = np.dot(M,Vv)
        # retrieve the forward model results, MVv
        path_to_vtu_file = str(k) + '/2d_canyon_1.vtu'
        vtu_data = vtktools.vtu(path_to_vtu_file)
        MVv = vtu_data.GetScalarField('Tracer') #vtu_data.GetScalarField(field)
#        print "gradJ: MVv[0:10]", MVv[0:10]

        HMVv = np.dot(H,MVv)
        Jmis = np.subtract(HVv,d)
        JmisM = np.subtract(HMVv,d)
        invR = np.linalg.inv(R)
        RJmis = np.dot(invR,Jmis)
        RJmisM = np.dot(invR,JmisM)
        HT = np.transpose(H)
        g1 = np.dot(HT,RJmis)
        g1M = np.dot(HT,RJmisM)
        ##MT = ... MT(g1M) = from importance map t_k+1 , map at t_k
        VT = np.transpose(V)
        ##VTMT = np.dot(VT,MT)
        g2 = np.dot(VT,g1)


        ggJ = v + g2 ##+ VTMT

        return ggJ

    #print "exectuable which has been selected:", opal_options.executable
    
    # ......... read the input .........
    
###############################################
## TRUNCATION AND REGULARIZATION PARAMETERS ###
###############################################
   # inputs
   n = 852
   lam = 1  #REGULARIZATION PARAMETER
   m = 45  #TRUNCATION PARAMETER FROM buildV.py
   xB = np.ones(n)
   y = np.ones(n)

   k = 8 # time at which observation is known

###############################################
########  INTIAL RUN OF FLUIDITY #############
###############################################
   # put checkpointing on for file k
   print "name of fwd_input_file", opal_options.data_assimilation.fwd_input_file
   libspud.load_options('2d_canyon.flml')#(opal_options.data_assimilation.fwd_input_file)

   # don't need these currently
   if libspud.have_option('io/checkpointing/checkpoint_at_start'):
       libspud.delete_option('io/checkpointing/checkpoint_at_start')
   if libspud.have_option('io/checkpointing/checkpoint_at_end'):
       libspud.delete_option('io/checkpointing/checkpoint_at_end')
   if libspud.have_option('io/checkpointing/checkpoint_period_in_dumps'):
       libspud.set_option('io/checkpointing/checkpoint_period_in_dumps',k)
   else:
      print "checkpoint_period_in_dumps option missing from xml file"
      sys.exit(0)

   libspud.write_options(opal_options.data_assimilation.fwd_input_file)
   libspud.clear_options() 

   string = opal_options.executable + " " + opal_options.data_assimilation.fwd_input_file


   # run code which will checkpoint every "k" dumps at the moment....
   print string
   os.system(string)


###############################################
########  COVARIANCE MATRICES     #############
###############################################


   V = np.loadtxt('matrixVprec'+str(m)+'.txt', usecols=range(m))

   R = lam * 0.5 * np.identity(n)

   H = np.identity(n)


###############################################
####### FROM PHYSICAL TO CONTROL SPACE ########
###############################################

   x0 = np.ones(n)
   Vin = np.linalg.pinv(V)
   v0 = np.dot(Vin,x0)


###############################################
#######       COMPUTE THE MISFIT       ########
###############################################


   VT = np.transpose(V)
   HxB = np.dot(H,xB)
   # consider multiple observations later - just one for now
   d = np.subtract(y,HxB)


###############################################
#######    COMPUTE THE MINIMUM OF J    ########
###############################################

   t = time.time()
   iter_count = 0
   Model_updated = False

   res = minimize(J, v0, method='L-BFGS-B', jac=gradJ,
                options={'disp': True})

###############################################
####### FROM CONTROL TO PHYSICAL SPACE ########
###############################################


   vDA = np.array([])
   vDA = res.x
   deltaxDA = np.dot(V,vDA)
   xDA = xB + deltaxDA

   elapsed = time.time() - t

   print " iter_count", iter_count

   #return 

###############################################
####### PRECONDITIONED COST FUNCTION J ########
###############################################



   return
def gen_flmls(params, template_dir, output_dir, paths, names, verbose):

    import types

    # get flml file from template_dir - first one we come across
    # If you have more in there, tough.
    full_flml = glob.glob(os.path.join(template_dir, '*.flml'))[0]
    # strip to the filename only
    flml = os.path.basename(full_flml)

    f = open(os.path.join(output_dir, 'runs', "directory_listing.csv"), "w")
    # append data to directory listing file
    line = "Directory number"
    for n in names:
        line = line + "," + n

    line = line + "\n"
    f.write(line)

    # loop over paramas
    # create a new directory, with a unqiue number, starting from 1
    # This makes it easier to use in an array job on CX1
    dir_num = 1
    for p_set in params:
        if (verbose):
            print "Processing " + str(dir_num)

        # copy contents from template folder to directory number
        dirname = os.path.join(output_dir, 'runs', str(dir_num))
        if (os.path.exists(os.path.join(dirname))):
            shutil.rmtree(dirname)
        shutil.copytree(template_dir, dirname)

        # open FLML file
        output_file = os.path.join(dirname, flml)
        # This load the data into the memory of the libspud library
        libspud.load_options(output_file)

        i = 0
        for path in paths:
            path = path.strip()
            # get type
            path_type = libspud.get_option_type(path)
            path_rank = libspud.get_option_rank(path)
            path_shape = libspud.get_option_shape(path)
            if (path_type is float and path_rank == 0):
                libspud.set_option(path, float(p_set[i]))
            elif (path_rank == 1 and path_type is float):
                value = eval(p_set[i])
                val = list(map(float, value))
                libspud.set_option(path, val)
            elif (path_rank == 2 and path_type is float):
                value = eval(p_set[i])
                val = []
                for row in value:
                    val.append(list(map(float, row)))
                libspud.set_option(path, val)

            i = i + 1

        # save file
        libspud.write_options(output_file)

        # append data to directory listing file
        line = str(dir_num)
        for p in p_set:
            # quoting the params so csv parsers can get the columns right
            line = line + "," + '"' + str(p) + '"'
        line = line + "\n"
        f.write(line)

        dir_num += 1

    f.close()
Exemple #5
0
def convert(fluidity_options_file_path, ff_options_file_path):

    # Read in Fluidity simulation options

    libspud.clear_options()
    libspud.load_options(fluidity_options_file_path)

    # Simulation name
    simulation_name = libspud.get_option("/simulation_name")

    # Geometry
    base = "/geometry"
    dimension = libspud.get_option(base + "/dimension")
    mesh_path = libspud.get_option(
        base + "/mesh::CoordinateMesh/from_file/file_name"
    ) + ".msh"  # FIXME: Always assumes gmsh format.

    # Function spaces
    velocity_function_space = FunctionSpace("/geometry", 1)
    freesurface_function_space = FunctionSpace("/geometry", 2)

    # Timestepping
    base = "/timestepping"
    current_time = libspud.get_option(base + "/current_time")
    timestep = libspud.get_option(base + "/timestep")
    finish_time = libspud.get_option(base + "/finish_time")

    ## Steady-state
    if (libspud.have_option(base + "/steady_state")):
        if (libspud.have_option(base + "/steady_state/tolerance")):
            steady_state = libspud.get_option(base + "/steady_state/tolerance")
        else:
            steady_state = 1e-7
    else:
        steady_state = None

    # I/O
    base = "/io"
    dump_format = libspud.get_option(base + "/dump_format")
    if (libspud.have_option(base + "/dump_period")):
        dump_period = libspud.get_option(base + "/dump_period/constant")
    elif (libspud.have_option(base + "/dump_period_in_timesteps")):
        dump_period = libspud.get_option(
            base + "/dump_period_in_timesteps/constant") * timestep
    else:
        print "Unable to obtain dump_period."
        sys.exit()

    # Gravity
    g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")

    # Velocity field (momentum equation)
    base = "/material_phase[0]/vector_field::Velocity"

    ## Depth (free surface mean height)
    c = libspud.get_child_name(
        base +
        "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/",
        1)
    depth = libspud.get_option(
        base +
        "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s"
        % c)

    ## Bottom drag coefficient
    if (libspud.have_option(base +
                            "/prognostic/equation::ShallowWater/bottom_drag")):
        c = libspud.get_child_name(
            base +
            "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/",
            1)
        bottom_drag = libspud.get_option(
            base +
            "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s"
            % c)
    else:
        bottom_drag = None

    ## Viscosity
    if (libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
        viscosity = libspud.get_option(
            base +
            "/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant"
        )[0][0]
    else:
        viscosity = None

    ## Momentum source
    if (libspud.have_option(base + "/prognostic/vector_field::Source")):
        c = libspud.get_child_name(
            base +
            "/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
        momentum_source = libspud.get_option(
            base +
            "/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" %
            c)
    else:
        momentum_source = None

    ## Initial condition
    if (libspud.have_option(base +
                            "/prognostic/initial_condition::WholeMesh")):
        c = libspud.get_child_name(
            base + "/prognostic/initial_condition::WholeMesh/", 1)
        velocity_initial_condition = libspud.get_option(
            base + "/prognostic/initial_condition::WholeMesh/%s" % c)
    else:
        velocity_initial_condition = 0.0

    ## Boundary conditions
    number_of_bcs = libspud.option_count(base +
                                         "/prognostic/boundary_conditions")
    velocity_bcs = []
    for i in range(number_of_bcs):
        velocity_bcs.append(
            VelocityBoundaryCondition(base +
                                      "/prognostic/boundary_conditions[%d]" %
                                      i))

    # Pressure field (continuity equation)
    base = "/material_phase[0]/scalar_field::Pressure"
    integrate_by_parts = libspud.have_option(
        base +
        "/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts"
    )

    ## Initial condition
    if (libspud.have_option(base +
                            "/prognostic/initial_condition::WholeMesh")):
        c = libspud.get_child_name(
            base + "/prognostic/initial_condition::WholeMesh/", 1)
        pressure_initial_condition = libspud.get_option(
            base + "/prognostic/initial_condition::WholeMesh/%s" % c)
    else:
        pressure_initial_condition = 0.0

    ## Boundary conditions
    number_of_bcs = libspud.option_count(base +
                                         "/prognostic/boundary_conditions")
    pressure_bcs = []
    for i in range(number_of_bcs):
        pressure_bcs.append(
            PressureBoundaryCondition(base +
                                      "/prognostic/boundary_conditions[%d]" %
                                      i))

    ## Continuity source
    if (libspud.have_option(base + "/prognostic/scalar_field::Source")):
        c = libspud.get_child_name(
            base +
            "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
        continuity_source = libspud.get_option(
            base +
            "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" %
            c)
    else:
        continuity_source = None

    # Write out to a Firedrake-Fluids simulation configuration file
    libspud.clear_options()

    # Create a bare-bones .swml file to add to.
    f = open(ff_options_file_path, "w")
    f.write("<?xml version='1.0' encoding='utf-8'?>\n")
    f.write("<shallow_water_options>\n")
    f.write("</shallow_water_options>\n")
    f.close()

    libspud.load_options(ff_options_file_path)

    # Simulation name
    libspud.set_option("/simulation_name", simulation_name)

    # Geometry
    base = "/geometry"
    libspud.set_option(base + "/dimension", dimension)
    libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)

    # Function spaces
    base = "/function_spaces"
    libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree",
                       velocity_function_space.degree)
    libspud.set_option(base + "/function_space::VelocityFunctionSpace/family",
                       velocity_function_space.family)
    libspud.set_option(
        base + "/function_space::FreeSurfaceFunctionSpace/degree",
        freesurface_function_space.degree)
    libspud.set_option(
        base + "/function_space::FreeSurfaceFunctionSpace/family",
        freesurface_function_space.family)

    # I/O
    base = "/io"
    libspud.set_option(base + "/dump_format", dump_format)
    libspud.set_option(base + "/dump_period", dump_period)

    # Timestepping
    base = "/timestepping"
    print timestep
    libspud.set_option(base + "/current_time", current_time)
    try:
        libspud.set_option(base + "/timestep", timestep)
    except:
        pass
    libspud.set_option(base + "/finish_time", finish_time)

    ## Steady-state
    if (steady_state):
        libspud.set_option(base + "/steady_state/tolerance", steady_state)

    # Gravity
    libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)

    # System/Core Fields: Velocity
    base = "/system/core_fields/vector_field::Velocity"

    ## Initial condition
    if (isinstance(velocity_initial_condition, str)):
        libspud.set_option(base + "/initial_condition/python",
                           velocity_initial_condition)
    else:
        libspud.set_option(base + "/initial_condition/constant",
                           velocity_initial_condition)

    ## Boundary conditions
    try:
        for i in range(len(velocity_bcs)):
            libspud.set_option(
                base +
                "/boundary_condition::%s/surface_ids" % velocity_bcs[i].name,
                velocity_bcs[i].surface_ids)
            libspud.set_option_attribute(
                base +
                "/boundary_condition::%s/type/name" % velocity_bcs[i].name,
                velocity_bcs[i].type)

            if (velocity_bcs[i].type == "dirichlet"):
                if (isinstance(velocity_bcs[i].value, str)):
                    libspud.set_option(
                        base +
                        "/boundary_condition::%s/type::dirichlet/value/python"
                        % velocity_bcs[i].name, velocity_bcs[i].value)
                else:
                    libspud.set_option(
                        base +
                        "/boundary_condition::%s/type::dirichlet/value/constant"
                        % velocity_bcs[i].name, velocity_bcs[i].value)
    except:
        pass

    # System/Core Fields: FreeSurfacePerturbation
    base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"

    #FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
    ## Initial condition
    if (isinstance(pressure_initial_condition, str)):
        libspud.set_option(base + "/initial_condition/python",
                           pressure_initial_condition)
    else:
        libspud.set_option(base + "/initial_condition/constant",
                           pressure_initial_condition)

    ## Boundary conditions
    try:
        for i in range(len(pressure_bcs)):
            libspud.set_option(
                base +
                "/boundary_condition::%s/surface_ids" % pressure_bcs[i].name,
                pressure_bcs[i].surface_ids)
            libspud.set_option(
                base +
                "/boundary_condition::%s/type/name" % pressure_bcs[i].name,
                pressure_bcs[i].type)

            if (pressure_bcs[i].type == "dirichlet"):
                if (isinstance(pressure_bcs[i].value, str)):
                    libspud.set_option(
                        base +
                        "/boundary_condition::%s/type::dirichlet/value/python"
                        % pressure_bcs[i].name, pressure_bcs[i].value)
                else:
                    libspud.set_option(
                        base +
                        "/boundary_condition::%s/type::dirichlet/value/constant"
                        % pressure_bcs[i].name, pressure_bcs[i].value)
    except:
        pass

    # System/Core Fields: FreeSurfaceMean
    base = "/system/core_fields/scalar_field::FreeSurfaceMean"
    if (isinstance(depth, str)):
        libspud.set_option(base + "/value/python", depth)
    else:
        libspud.set_option(base + "/value/constant", depth)

    # Equations: Continuity equation
    base = "/system/equations/continuity_equation"
    libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)

    ## Source term
    if (continuity_source is not None):
        if (isinstance(continuity_source, str)):
            libspud.set_option(
                base + "/source_term/scalar_field::Source/value/python",
                continuity_source)
        else:
            libspud.set_option(
                base + "/source_term/scalar_field::Source/value/constant",
                continuity_source)

    # Equations: Momentum equation
    base = "/system/equations/momentum_equation"

    ## Viscosity
    if (viscosity is not None):
        if (isinstance(viscosity, str)):
            libspud.set_option(
                base + "/stress_term/scalar_field::Viscosity/value/python",
                viscosity)
        else:
            libspud.set_option(
                base + "/stress_term/scalar_field::Viscosity/value/constant",
                viscosity)

    ## Bottom drag
    if (bottom_drag is not None):
        if (isinstance(bottom_drag, str)):
            libspud.set_option(
                base +
                "/drag_term/scalar_field::BottomDragCoefficient/value/python",
                bottom_drag)
        else:
            libspud.set_option(
                base +
                "/drag_term/scalar_field::BottomDragCoefficient/value/constant",
                bottom_drag)

    ## Source term
    if (momentum_source is not None):
        if (isinstance(momentum_source, str)):
            libspud.set_option(
                base + "/source_term/vector_field::Source/value/python",
                momentum_source)
        else:
            libspud.set_option(
                base + "/source_term/vector_field::Source/value/constant",
                momentum_source)

    # Write all the applied options to file.
    libspud.write_options(ff_options_file_path)

    return
libspud.delete_option('/foo')
assert libspud.option_count('/foo') == 0

try:
  libspud.get_option('/foo')
  assert False
except libspud.SpudKeyError, e:
  pass

try:
  libspud.get_option('/geometry')
  assert False
except libspud.SpudTypeError, e:
  pass

libspud.write_options('test_out.flml')

try:
  libspud.set_option('/test', 4.3)
except libspud.SpudNewKeyWarning, e:
  pass

assert libspud.get_option('/test') == 4.3

libspud.set_option('/test',4)

assert libspud.get_option('/test') == 4

libspud.set_option('/test',[[4.0,2.0,3.0],[2.0,5.0,6.6]]) 

assert libspud.get_option('/test') == [[4.0,2.0,3.0],[2.0,5.0,6.6]]
def gen_flmls(params, template_dir, output_dir, paths, names, verbose):

    import types

    # get flml file from template_dir - first one we come across
    # If you have more in there, tough.
    full_flml = glob.glob(os.path.join(template_dir,'*.flml'))[0]
    # strip to the filename only
    flml = os.path.basename(full_flml)

    f = open(os.path.join(output_dir,'runs',"directory_listing.csv"),"w")
    # append data to directory listing file
    line = "Directory number"
    for n in names:
        line = line+","+n

    line = line + "\n"
    f.write(line)

    # loop over paramas
    # create a new directory, with a unqiue number, starting from 1
    # This makes it easier to use in an array job on CX1
    dir_num = 1
    for p_set in params:
        if (verbose):
            print "Processing "+str(dir_num)

        # copy contents from template folder to directory number
        dirname = os.path.join(output_dir,'runs',str(dir_num))
        if (os.path.exists(os.path.join(dirname))):
            shutil.rmtree(dirname)
        shutil.copytree(template_dir,dirname)

        # open FLML file
        output_file = os.path.join(dirname,flml)
        # This load the data into the memory of the libspud library
        libspud.load_options(output_file)

        i = 0
        for path in paths:
            path = path.strip()
            # get type
            path_type = libspud.get_option_type(path)
            path_rank = libspud.get_option_rank(path)
            path_shape = libspud.get_option_shape(path)
            if (path_type is float and path_rank == 0):
                libspud.set_option(path,float(p_set[i]))
            elif (path_rank == 1 and path_type is float):
                value = eval(p_set[i])
                val = list(map(float, value))
                libspud.set_option(path,val)
            elif (path_rank == 2 and path_type is float):
                value = eval(p_set[i])
                val = []
                for row in value:
                    val.append(list(map(float, row)))
                libspud.set_option(path,val)

            i = i+1

        # save file
        libspud.write_options(output_file)
            
        # append data to directory listing file
        line = str(dir_num)
        for p in p_set:
            # quoting the params so csv parsers can get the columns right
            line = line+","+'"'+str(p)+'"'
        line = line +"\n"
        f.write(line)

        dir_num += 1


    f.close()
Exemple #8
0
libspud.set_option('/problem_type', 'helloworld')
test("libspud.get_option('/problem_type') == 'helloworld'")

exception_test("libspud.set_option_attribute('/foo/bar', 'foobar')",
               libspud.SpudNewKeyWarning)

test("libspud.get_option('/foo/bar') == 'foobar'")

libspud.delete_option('/foo')
test("libspud.option_count('/foo') == 0")

exception_test("libspud.get_option('/foo')", libspud.SpudKeyError)
exception_test("libspud.get_option('/geometry')", libspud.SpudTypeError)

libspud.write_options(dirpath + 'test_out.flml')

exception_test("libspud.set_option('/test', 4.3)", libspud.SpudNewKeyWarning)
test("libspud.get_option('/test') == 4.3")
test("libspud.set_option('/test',4) or True")

test("libspud.get_option('/test') == 4")

libspud.set_option('/test', [[4.0, 2.0, 3.0], [2.0, 5.0, 6.6]])

test("libspud.get_option('/test') == [[4.0,2.0,3.0],[2.0,5.0,6.6]]")

libspud.set_option('/test', "Hallo")

test("libspud.get_option('/test') == 'Hallo'")
Exemple #9
0
import libspud
import shutil

class flml_things:
    "list of things to change in an flml file"

    def __init__(self,name='',mesh='',dt=0.2):
        self.name = name
        self.dt = dt
        self.mesh = mesh

parent_file = 'diffusion_dg1'
diffusion_dg_A = flml_things(name='diffusion_dg_A',mesh='MMS_A',dt=0.2)
diffusion_dg_B = flml_things(name='diffusion_dg_B',mesh='MMS_B',dt=0.2)
diffusion_dg_C = flml_things(name='diffusion_dg_C',mesh='MMS_C',dt=0.2)
diffusion_dg_D = flml_things(name='diffusion_dg_D',mesh='MMS_D',dt=0.2)
diffusion_dg_E = flml_things(name='diffusion_dg_E',mesh='MMS_E',dt=0.2)
filelist = [diffusion_dg_A,diffusion_dg_B,diffusion_dg_C,diffusion_dg_D,diffusion_dg_E]

for file in filelist:
    shutil.copy(parent_file+'.flml',file.name+'.flml')
    libspud.load_options(file.name+'.flml')
    libspud.set_option('/simulation_name', file.name)
    libspud.set_option('/geometry/mesh[@name="CoordinateMesh"]/from_file/file_name', file.mesh)
    libspud.set_option('/timestepping/timestep', file.dt)

    libspud.write_options(file.name+'.flml')
Exemple #10
0
def convert(fluidity_options_file_path, ff_options_file_path):
   
   # Read in Fluidity simulation options
   
   libspud.clear_options()
   libspud.load_options(fluidity_options_file_path)
   
   # Simulation name
   simulation_name = libspud.get_option("/simulation_name")
   
   # Geometry
   base = "/geometry"
   dimension = libspud.get_option(base + "/dimension")
   mesh_path = libspud.get_option(base + "/mesh::CoordinateMesh/from_file/file_name") + ".msh" # FIXME: Always assumes gmsh format.
  
   # Function spaces
   velocity_function_space = FunctionSpace("/geometry", 1)
   freesurface_function_space = FunctionSpace("/geometry", 2)
    
   # Timestepping
   base = "/timestepping"
   current_time = libspud.get_option(base + "/current_time")
   timestep = libspud.get_option(base + "/timestep")
   finish_time = libspud.get_option(base + "/finish_time")

   ## Steady-state
   if(libspud.have_option(base + "/steady_state")):
      if(libspud.have_option(base + "/steady_state/tolerance")):
         steady_state = libspud.get_option(base + "/steady_state/tolerance")
      else:
         steady_state = 1e-7
   else:
      steady_state = None   

   # I/O
   base = "/io"
   dump_format = libspud.get_option(base + "/dump_format")
   if(libspud.have_option(base + "/dump_period")):
      dump_period = libspud.get_option(base + "/dump_period/constant")
   elif(libspud.have_option(base + "/dump_period_in_timesteps")):
      dump_period = libspud.get_option(base + "/dump_period_in_timesteps/constant")*timestep
   else:
      print "Unable to obtain dump_period."
      sys.exit()
      
   # Gravity
   g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")
   
   # Velocity field (momentum equation)
   base = "/material_phase[0]/vector_field::Velocity"
   
   ## Depth (free surface mean height)
   c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/", 1)
   depth = libspud.get_option(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s" % c)
   
   ## Bottom drag coefficient
   if(libspud.have_option(base + "/prognostic/equation::ShallowWater/bottom_drag")):
      c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/", 1)
      bottom_drag = libspud.get_option(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s" % c)
   else:
      bottom_drag = None
      
   ## Viscosity
   if(libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
      viscosity = libspud.get_option(base + "/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant")[0][0]
   else:
      viscosity = None

   ## Momentum source
   if(libspud.have_option(base + "/prognostic/vector_field::Source")):
      c = libspud.get_child_name(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
      momentum_source = libspud.get_option(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" % c)
   else:
      momentum_source = None
      
   ## Initial condition
   if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
      c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
      velocity_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
   else:
      velocity_initial_condition = 0.0
      
   ## Boundary conditions
   number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
   velocity_bcs = []
   for i in range(number_of_bcs):
      velocity_bcs.append(VelocityBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
   
   
   # Pressure field (continuity equation)
   base = "/material_phase[0]/scalar_field::Pressure"
   integrate_by_parts = libspud.have_option(base + "/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts")
   
   ## Initial condition
   if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
      c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
      pressure_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
   else:
      pressure_initial_condition = 0.0
      
   ## Boundary conditions
   number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
   pressure_bcs = []
   for i in range(number_of_bcs):
      pressure_bcs.append(PressureBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
   
   ## Continuity source
   if(libspud.have_option(base + "/prognostic/scalar_field::Source")):
      c = libspud.get_child_name(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
      continuity_source = libspud.get_option(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" % c)
   else:
      continuity_source = None
   





   
   
   # Write out to a Firedrake-Fluids simulation configuration file
   libspud.clear_options()
   
   # Create a bare-bones .swml file to add to.
   f = open(ff_options_file_path, "w")
   f.write("<?xml version='1.0' encoding='utf-8'?>\n")
   f.write("<shallow_water_options>\n")
   f.write("</shallow_water_options>\n")
   f.close()
   
   libspud.load_options(ff_options_file_path)

   # Simulation name
   libspud.set_option("/simulation_name", simulation_name)
   
   # Geometry
   base = "/geometry"
   libspud.set_option(base + "/dimension", dimension)
   libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)
   
   # Function spaces
   base = "/function_spaces"
   libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree", velocity_function_space.degree)
   libspud.set_option(base + "/function_space::VelocityFunctionSpace/family", velocity_function_space.family)
   libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/degree", freesurface_function_space.degree)
   libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/family", freesurface_function_space.family)
   
   # I/O
   base = "/io"
   libspud.set_option(base + "/dump_format", dump_format)
   libspud.set_option(base + "/dump_period", dump_period)
   
   # Timestepping
   base = "/timestepping"
   print timestep
   libspud.set_option(base + "/current_time", current_time)
   try:
      libspud.set_option(base + "/timestep", timestep)
   except:
      pass
   libspud.set_option(base + "/finish_time", finish_time)
   
   ## Steady-state
   if(steady_state):
      libspud.set_option(base + "/steady_state/tolerance", steady_state)
      
   # Gravity
   libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)
   
   # System/Core Fields: Velocity
   base = "/system/core_fields/vector_field::Velocity"
   
   ## Initial condition
   if(isinstance(velocity_initial_condition, str)):
      libspud.set_option(base + "/initial_condition/python", velocity_initial_condition)
   else:
      libspud.set_option(base + "/initial_condition/constant", velocity_initial_condition)
   
   ## Boundary conditions
   try:
      for i in range(len(velocity_bcs)):
         libspud.set_option(base + "/boundary_condition::%s/surface_ids" % velocity_bcs[i].name, velocity_bcs[i].surface_ids)
         libspud.set_option_attribute(base + "/boundary_condition::%s/type/name" % velocity_bcs[i].name, velocity_bcs[i].type)
         
         if(velocity_bcs[i].type == "dirichlet"):
            if(isinstance(velocity_bcs[i].value, str)):
               libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % velocity_bcs[i].name, velocity_bcs[i].value)
            else:
               libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % velocity_bcs[i].name, velocity_bcs[i].value)
   except:
      pass

   # System/Core Fields: FreeSurfacePerturbation
   base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"
   
   #FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
   ## Initial condition
   if(isinstance(pressure_initial_condition, str)):
      libspud.set_option(base + "/initial_condition/python", pressure_initial_condition)
   else:
      libspud.set_option(base + "/initial_condition/constant", pressure_initial_condition)
   
   ## Boundary conditions
   try:
      for i in range(len(pressure_bcs)):
         libspud.set_option(base + "/boundary_condition::%s/surface_ids" % pressure_bcs[i].name, pressure_bcs[i].surface_ids)
         libspud.set_option(base + "/boundary_condition::%s/type/name" % pressure_bcs[i].name, pressure_bcs[i].type)
         
         if(pressure_bcs[i].type == "dirichlet"):
            if(isinstance(pressure_bcs[i].value, str)):
               libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % pressure_bcs[i].name, pressure_bcs[i].value)
            else:
               libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % pressure_bcs[i].name, pressure_bcs[i].value)
   except:
      pass

   # System/Core Fields: FreeSurfaceMean
   base = "/system/core_fields/scalar_field::FreeSurfaceMean"
   if(isinstance(depth, str)):
      libspud.set_option(base + "/value/python", depth)
   else:
      libspud.set_option(base + "/value/constant", depth)
      
   
   # Equations: Continuity equation
   base = "/system/equations/continuity_equation"
   libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)

   ## Source term
   if(continuity_source is not None):
      if(isinstance(continuity_source, str)):
         libspud.set_option(base + "/source_term/scalar_field::Source/value/python", continuity_source)
      else:
         libspud.set_option(base + "/source_term/scalar_field::Source/value/constant", continuity_source)
         
   # Equations: Momentum equation
   base = "/system/equations/momentum_equation"
   
   ## Viscosity
   if(viscosity is not None):
      if(isinstance(viscosity, str)):
         libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/python", viscosity)
      else:
         libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/constant", viscosity)

   ## Bottom drag
   if(bottom_drag is not None):
      if(isinstance(bottom_drag, str)):
         libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/python", bottom_drag)
      else:
         libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/constant", bottom_drag)
   
   ## Source term
   if(momentum_source is not None):
      if(isinstance(momentum_source, str)):
         libspud.set_option(base + "/source_term/vector_field::Source/value/python", momentum_source)
      else:
         libspud.set_option(base + "/source_term/vector_field::Source/value/constant", momentum_source)
   
   
   # Write all the applied options to file.
   libspud.write_options(ff_options_file_path)
   
   return