コード例 #1
0
ファイル: checkpoint.py プロジェクト: xuexianwu/anuga_core
def load_checkpoint_file(domain_name="domain", checkpoint_dir=".", time=None):

    from os.path import join

    if numprocs > 1:
        domain_name = domain_name + "_P{}_{}".format(numprocs, myid)

    if time is None:
        # will pull out the last available time
        times = _get_checkpoint_times(domain_name, checkpoint_dir)

        times = list(times)
        times.sort()
        # print times
    else:
        times = [float(time)]

    if len(times) == 0:
        raise Exception, "Unable to open checkpoint file"

    for time in reversed(times):

        pickle_name = join(checkpoint_dir, domain_name) + "_" + str(time) + ".pickle"
        # print pickle_name

        try:
            import cPickle

            domain = cPickle.load(open(pickle_name, "rb"))
            success = True
        except:
            success = False

        # print success
        overall = success
        for cpu in range(numprocs):
            if cpu != myid:
                send(success, cpu)

        for cpu in range(numprocs):
            if cpu != myid:
                overall = overall & receive(cpu)

        barrier()

        # print myid, overall, success, time

        if overall:
            break

    if not overall:
        raise Exception, "Unable to open checkpoint file"

    domain.last_walltime = walltime()
    domain.communication_time = 0.0
    domain.communication_reduce_time = 0.0
    domain.communication_broadcast_time = 0.0

    return domain
コード例 #2
0
def load_checkpoint_file(domain_name='domain', checkpoint_dir='.', time=None):

    from os.path import join

    if numprocs > 1:
        domain_name = domain_name + '_P{}_{}'.format(numprocs, myid)

    if time is None:
        # will pull out the last available time
        times = _get_checkpoint_times(domain_name, checkpoint_dir)

        times = list(times)
        times.sort()
        #print times
    else:
        times = [float(time)]

    if len(times) == 0: raise Exception("Unable to open checkpoint file")

    for time in reversed(times):

        pickle_name = join(checkpoint_dir,
                           domain_name) + '_' + str(time) + '.pickle'
        #print pickle_name

        try:
            try:
                import dill as pickle
            except:
                import pickle
            domain = pickle.load(open(pickle_name, 'rb'))
            success = True
        except:
            success = False

        #print success
        overall = success
        for cpu in range(numprocs):
            if cpu != myid:
                send(success, cpu)

        for cpu in range(numprocs):
            if cpu != myid:
                overall = overall & receive(cpu)

        barrier()

        #print myid, overall, success, time

        if overall: break

    if not overall: raise Exception("Unable to open checkpoint file")

    domain.last_walltime = walltime()
    domain.communication_time = 0.0
    domain.communication_reduce_time = 0.0
    domain.communication_broadcast_time = 0.0

    return domain
コード例 #3
0
    def _setup_original_domain(self, np=None):
        """
        Create sequential domain and partition
        
        """
        verbose = self.verbose
        outname = self.outname
        partition_dir = self.partition_dir
        
        if np is None:
            np = numprocs
        
        # Only create the sequential domain on processor 0
        if myid == 0:
            
            if verbose: print 'CREATING PARTITIONED DOMAIN'
            
            # Let's see if we have already pickled this domain
            pickle_name = outname+'_P%g_%g.pickle'% (1,0)
            pickle_name = join(partition_dir,pickle_name)
    
            if os.path.exists(pickle_name):
                if verbose: print 'Saved domain seems to already exist'
            else:
                domain = self.setup_domain(self)
                
                if verbose: print 'Saving Domain'
                sequential_distribute_dump(domain, 1, partition_dir=partition_dir, verbose=verbose)    

            
            # Now partition the domain

            
            if verbose: print 'Load in saved sequential pickled domain'
            domain = sequential_distribute_load_pickle_file(pickle_name, np=1, verbose = verbose)
         
            par_pickle_name = outname+'_P%g_%g.pickle'% (np,0)
            par_pickle_name = join(partition_dir,par_pickle_name)
            if os.path.exists(par_pickle_name):
                if verbose: print 'Saved partitioned domain seems to already exist'
            else:
                if verbose: print 'Dump partitioned domains'
                sequential_distribute_dump(domain, np, partition_dir=partition_dir, verbose=verbose) 

        barrier()
        
        #===============================================================================
        # Setup parallel domain
        #===============================================================================
        if myid == 0 and verbose: print 'LOADING PARTITIONED DOMAIN'
        
        self.domain = sequential_distribute_load(filename=join(partition_dir,outname), verbose = self.verbose)
コード例 #4
0
ファイル: simulation.py プロジェクト: samcom12/towradgi
    def run(self, yieldstep=None, finaltime=None):

        if yieldstep is None:
            yieldstep = self.args.yieldstep

        if finaltime is None:
            finaltime = self.args.finaltime

        if myid == 0 and self.verbose:
            print 'EVOLVE(yieldstep = {}, finaltime = {})'.format(
                yieldstep, finaltime)

        domain = self.domain
        #import time
        t0 = time.time()

        for t in domain.evolve(yieldstep=yieldstep,
                               finaltime=finaltime):  #= 83700.):

            if myid == 0 and self.verbose:
                domain.write_time()

        barrier()
        for p in range(numprocs):
            if myid == p:
                print 'Processor %g ' % myid
                print 'That took %.2f seconds' % (time.time() - t0)
                print 'Communication time %.2f seconds' % domain.communication_time
                print 'Reduction Communication time %.2f seconds' % domain.communication_reduce_time
                print 'Broadcast time %.2f seconds' % domain.communication_broadcast_time
            else:
                pass

            barrier()


#         if myid == 0 and self.verbose:
#             print 'Number of processors %g ' %numprocs
#             print 'That took %.2f seconds' %(time.time()-t0)
#             print 'Communication time %.2f seconds'%domain.communication_time
#             print 'Reduction Communication time %.2f seconds'%domain.communication_reduce_time
#             print 'Broadcast time %.2f seconds'%domain.communication_broadcast_time

        finalize()
コード例 #5
0
    def run(self, yieldstep = None, finaltime =None):
        
        if yieldstep is None:
            yieldstep = self.args.yieldstep
            
        if finaltime is None:
            finaltime = self.args.finaltime
            
        if myid == 0 and self.verbose: 
            print 'EVOLVE(yieldstep = {}, finaltime = {})'.format(yieldstep,finaltime)
        
        
        domain = self.domain
        #import time
        t0 = time.time()
            
        for t in domain.evolve(yieldstep = yieldstep, finaltime = finaltime):#= 83700.):
        
            if myid == 0 and self.verbose:
                domain.write_time()
        
        barrier()
        for p in range(numprocs):
            if myid == p:
                print 'Processor %g ' %myid
                print 'That took %.2f seconds' %(time.time()-t0)
                print 'Communication time %.2f seconds'%domain.communication_time
                print 'Reduction Communication time %.2f seconds'%domain.communication_reduce_time
                print 'Broadcast time %.2f seconds'%domain.communication_broadcast_time
            else:
                pass
        
            barrier()

#         if myid == 0 and self.verbose:
#             print 'Number of processors %g ' %numprocs
#             print 'That took %.2f seconds' %(time.time()-t0)
#             print 'Communication time %.2f seconds'%domain.communication_time
#             print 'Reduction Communication time %.2f seconds'%domain.communication_reduce_time
#             print 'Broadcast time %.2f seconds'%domain.communication_broadcast_time
        
    
        finalize()
コード例 #6
0
ファイル: parallel_job.py プロジェクト: chrimerss/anuga_core
    domain.set_quantity('KE', 0.5, location='centroids')
    domain.set_quantity('coeM', 0.5, location='centroids')
    domain.set_quantity('expM', 0.5, location='centroids')
    domain.set_quantity('coeR', 0.5, location='centroids')
    domain.set_quantity('coeS', 0.5, location='centroids')
    domain.set_quantity('KS', 0.5, location='centroids')
    domain.set_quantity('KI', 0.5, location='centroids')

    Br = anuga.Reflective_boundary(domain)
    Bt = anuga.Transmissive_boundary(domain)

    domain.set_boundary({'bottom': Bt, 'exterior': Br})
else:
    domain = None

barrier()

domain = distribute(domain)

#domain.set_evap_dir('/hydros/MengyuChen/pet', pattern='cov_et17%m%d.asc', freq='D')
#domain.set_precip_dir('/home/ZhiLi/CRESTHH/data/precip',pattern='imerg%Y%m%dS%H%M%S.tif', freq='H')
#domain.set_timestamp('20170825180000', format='%Y%m%d%H%M%S')
#domain.set_time_interval('1H')

domain.set_evap_dir('/hydros/MengyuChen/pet',
                    pattern='cov_et17%m%d.asc',
                    freq='1D')
# domain.set_precip_dir('/home/ZhiLi/CRESTHH/data/precip',pattern='nimerg%Y%m%dS%H%M%S.tif', freq='H')
domain.set_precip_dir(
    '/hydros/MengyuChen/mrmsPrecRate',
    pattern='PrecipRate_00.00_%Y%m%d-%H%M00.grib2-var0-z0.tif',
コード例 #7
0
ファイル: riverwall.py プロジェクト: corsima/anuga_core
    def export_riverwalls_to_text(self, output_dir=None):
        """
            Function for dumping riverwall outputs to text file (useful for QC)

            This will overwrite any existing files with the same location/name

            INPUT: output_dir = Directory where the outputs will be written

            OUTPUT:
                    None, but writes files as a side effect

        """
        if (output_dir is None):
            return

        if (myid == 0):
            # Make output directory
            try:
                os.mkdir(output_dir)
            except:
                pass
            # Make output files with empty contents
            for i, riverWallFile in enumerate(self.names):
                newFile = open(
                    output_dir + '/' +
                    os.path.splitext(os.path.basename(riverWallFile))[0] +
                    '.txt', 'w')
                # Write hydraulic variable information
                hydraulicVars = self.hydraulic_properties[i, :]
                newFile.write('## Hydraulic Variable values below ## \n')
                newFile.write(str(self.hydraulic_variable_names) + '\n')
                newFile.write(str(hydraulicVars) + '\n')
                newFile.write('\n')
                newFile.write(
                    '## xyElevation at edges below. Order may be erratic for parallel runs ##\n'
                )
                newFile.close()
        else:
            pass

        domain = self.domain

        # The other processes might try to write into file
        # before process 0 has created file, so we need a
        # barrier
        if domain.parallel: barrier()

        # Now dump the required info to the files
        for i in range(numprocs):
            # Write 1 processor at a time
            if (myid == i):
                for j, riverWallname in enumerate(self.names):
                    # Get xyz data for riverwall j
                    riverWallInds = (self.hydraulic_properties_rowIndex == j
                                     ).nonzero()[0].tolist()
                    riverWallDomainInds = self.riverwall_edges[
                        riverWallInds].tolist()
                    myXCoords = domain.edge_coordinates[
                        riverWallDomainInds,
                        0] + domain.geo_reference.xllcorner
                    myYCoords = domain.edge_coordinates[
                        riverWallDomainInds,
                        1] + domain.geo_reference.yllcorner
                    myElev = self.riverwall_elevation[riverWallInds]

                    # Open file for appending data
                    theFile = open(
                        output_dir + '/' +
                        os.path.splitext(os.path.basename(riverWallname))[0] +
                        '.txt', 'a')
                    for k in range(len(myElev)):
                        theFile.write(
                            str(myXCoords[k]) + ',' + str(myYCoords[k]) + ',' +
                            str(myElev[k]) + '\n')
                    theFile.close()

            else:
                pass

        return
コード例 #8
0
ファイル: riverwall.py プロジェクト: corsima/anuga_core
    def create_riverwalls(self,
                          riverwalls,
                          riverwallPar={},
                          default_riverwallPar={},
                          tol=1.0e-4,
                          verbose=True,
                          output_dir=None):
        """Add riverwalls at chosen locations along the mesh

        As of 22/04/2014, these only work with DE algorithms [for which the concept is natural]

        The walls MUST EXACTLY COINCIDE with edges along the mesh 
        
        You can force the mesh to do this by passing riverwalls.values() 
        to the 'breaklines' argument in the function create_mesh_from_regions. You
        may also need to set the maximum_triangle_area for regions, if the breaklines
        split the region.  Do this with the regionPtArea argument in
        create_mesh_from_regions.

        As of 22/04/2014, the computational method used here is very 'brute-force'
        For each segment on each riverwall, every point in the mesh is checked to see
        if it is on the segment. A possibly faster/less memory method would be to
        'walk' through connected edges on the mesh.

        Inputs:
            riverwalls: Dictionary of '3D polygons', containing xyz locations of named riverwalls.

                exampleRiverWalls = { # Left bank n1 -- 
                                      'n1': [[1.0, 1000., 2.],
                                             [1.0, 50., 3.]],
                                      # Left bank n2 
                                       'n2': [[2.0, 30., 1.0],
                                              [3.0, 20., 2.], 
                                              [2.5, 15., 1.5]]
                                    }

            riverwallPar: Dictionary containing a dictionary of named hydraulic parameters for each named riverwall
                          If parameters are not provided, default values will be used. 
                          See the help for class 'RiverWall' for an explanation of these

                exampleRiverWallPar = {'n2': {'Qfactor':0.5} }
                    This would use a Qfactor of 0.5 for riverwall 'n2', while the other riverwall would have the default values

            default_riverwallPar:  Dictionary containing default values of the riverwall parameters, to be used
                                   if they are not explicitly set.
                                   If not provided, defaults from __init__ are used. See the help for class 'RiverWall' for more info

                example_default_riverwallPar = {'Qfactor':1.5,  
                                                's1': 0.9,      
                                                's2': 0.95,     
                                                'h1': 1.0,      
                                                'h2': 1.5       
                                               }

                example_default_riverwallPar = {'Qfactor':1.5,  
                                                's1': 10000.,      
                                                's2': 20000.     
                                               } # Here h1/h2 defaults will come from __init__
                 

            tol: Edges will be assigned a riverwall elevation if they are within 'tol' of
                 a segment in riverwalls. Round-off error means this should not be too small.

            verbose: TRUE/FALSE Print lots of information

            output_dir: Text representation of riverwalls is written to output_dir, unless output_dir=None

        Outputs:
            None, but it sets domain.edge_flux_type = 1 for every edge on a riverwall
            Also, it adds a RiverWall object domain.riverwallData to the domain
            The latter contains the riverwall heights, names, and hydraulic properties for each edge, in
              a way we can pass in/out of C code.

        """

        #if(verbose and myid==0):
        #    print ' '
        #    print 'WARNING: Riverwall is an experimental feature'
        #    print '         At each riverwall edge, we place a thin "wall" between'
        #    print '         the 2 edges -- so each sees its neighbour edge as having'
        #    print '         bed elevation = max(levee height, neighbour bed elevation)'
        #    print '         We also force the discharge with a weir relation, blended with'
        #    print '         the shallow water flux solution as the ratio (min_head)/(weir_height) becomes '
        #    print '         large, or the ratio (downstream_head)/(upstream_head) becomes large'
        #    print ' '
        #    print '  It works in parallel, but you must use domain.riverwallData.create_riverwall AFTER distributing the mesh'
        #    print ' '

        # NOTE: domain.riverwallData is initialised in shallow_water_domain.py for DE algorithms
        domain = self.domain

        # Check flow algorithm
        if (not domain.get_using_discontinuous_elevation()):
            raise Exception, 'Riverwalls are currently only supported for discontinuous elevation flow algorithms'

        if (len(self.names) > 0):
            # Delete any existing riverwall data
            # The function cannot presently be used to partially edit riverwall data
            if (verbose):
                print 'Warning: There seems to be existing riverwall data'
                print 'It will be deleted and overwritten with this function call'
            domain.riverwallData.__init__(domain)

        # Store input parameters
        # FIXME: Is this worth it?
        self.input_riverwall_geo = riverwalls
        self.input_riverwallPar = riverwallPar

        # Update self.default_riverwallPar (defined in __init__)
        for i in self.default_riverwallPar.keys():
            if (default_riverwallPar.has_key(i)):
                self.default_riverwallPar[i] = default_riverwallPar[i]

        # Check that all the keys in default_riverwallPar are allowed
        for i in default_riverwallPar.keys():
            if (not self.default_riverwallPar.has_key(i)):
                msg = 'Key ', i + ' in default_riverwallPar not recognized'
                raise Exception, msg
        # Final default river-wall parameters
        default_riverwallPar = self.default_riverwallPar

        # Check that all named inputs in riverwallPar correspond to names in
        # riverwall
        for i in riverwallPar.keys():
            if not riverwalls.has_key(i):
                msg = 'Key ', i, ' in riverwallPar has no corresponding key in riverwall'
                raise Exception, msg
            #
            # Check that all hydraulic parameter names in riverwallPar correspond
            # to names in default_riverwallPar
            #
            for j in riverwallPar[i].keys():
                if not default_riverwallPar.has_key(j):
                    msg = 'Hydraulic parameter named ', j ,\
                          ' not recognised in default_riverwallPar'
                    raise Exception, msg

        if (verbose):
            print 'Setting riverwall elevations (P' + str(myid) + ')...'

        # Set up geometry
        exy = domain.edge_coordinates
        llx = domain.mesh.geo_reference.get_xllcorner()
        lly = domain.mesh.geo_reference.get_yllcorner()

        # Temporary variables
        from anuga.config import max_float
        riverwall_elevation = exy[:, 0] * 0. - max_float
        riverwall_Qfactor = exy[:, 0] * 0.
        riverwall_rowIndex = exy[:, 0] * 0 - 1.
        riverwall_rowIndex.astype(int)

        # Loop over all segments in each riverwall, and set its elevation
        nw = range(len(riverwalls))
        nw_names = riverwalls.keys(
        )  # Not guarenteed to be in deterministic order

        if (verbose):
            # Use variable to record messages, allows cleaner parallel printing
            printInfo = ''

        for i in nw:
            # Name of riverwall
            riverwalli_name = nw_names[i]
            # Look at the ith riverwall
            riverwalli = riverwalls[riverwalli_name]

            ns = len(riverwalli) - 1

            if (verbose):
                printInfo = printInfo + '  Wall ' + str(i) + ' ....\n'

            for j in range(ns):
                if (verbose):
                    printInfo = printInfo + '    Segment ' + str(j) + ' ....\n'
                # Start and end xyz coordinates
                start = riverwalli[j]
                end = riverwalli[j + 1]

                if (len(start) != 3 | len(end) != 3):
                    msg = 'Each riverwall coordinate must have at exactly 3 values [xyz]'
                    raise Exception, msg

                # Find length
                segLen = ((start[0] - end[0])**2 + (start[1] - end[1])**2)**0.5
                if (segLen < tol):
                    if (verbose):
                        printInfo = printInfo + '  Segment with length < tolerance ' + str(
                            tol) + ' ignored\n'
                    continue

                # Find edge indices which are within 'tol' of the segment
                # We use a simple, inefficient method [but likely ok in practice
                # except for very complex riverwalls]

                # Unit vector along segment
                se_0 = -(start[0] - end[0]) / segLen
                se_1 = -(start[1] - end[1]) / segLen

                # Vector from 'start' to every point on mesh
                # NOTE: We account for georeferencing
                pv_0 = exy[:, 0] - (start[0] - llx)
                pv_1 = exy[:, 1] - (start[1] - lly)

                pvLen = (pv_0**2 + pv_1**2)**0.5

                # Dot product of pv and se == along-segment distance of projection
                # of each point onto segment
                pv_dot_se = pv_0 * se_0 + pv_1 * se_1
                # Normal distance^2 of each point to segment
                perp_len_sq = pvLen**2. - pv_dot_se**2.

                # Point is on a levee if the perpendicular distance is < tol,
                # AND it is between start and end [within a tolerance]
                onLevee = (perp_len_sq < tol**2) * (pv_dot_se > 0. - tol) * (
                    pv_dot_se < segLen + tol)
                onLevee = onLevee.nonzero()
                onLevee = onLevee[0]
                if (len(onLevee) == 0):
                    continue

                if (verbose):
                    printInfo = printInfo + '       Finding ' + str(
                        len(onLevee)) + ' edges on this segment\n'

                # Levee has Edge_flux_type=1
                domain.edge_flux_type[onLevee] = 1

                # Get edge elevations as weighted averages of start/end elevations
                w0 = pv_dot_se[onLevee] / segLen
                w0 = w0 * (w0 >= 0.0)  # Enforce min of 0
                w0 = w0 * (w0 <= 1.0) + 1.0 * (w0 > 1.0)  # Max of 1
                riverwall_elevation[onLevee] = start[2] * (1.0 -
                                                           w0) + w0 * end[2]

                # Record row index
                riverwall_rowIndex[onLevee] = i

        # Now, condense riverwall_elevation to array with length = number of riverwall edges
        #
        #  We do this to avoid storing a riverwall_elevation for every edge in the mesh
        #  However, the data structure ends up being quite complex -- maybe there is a better way?
        #
        # The zeroth index in domain.edge_flux_type which = 1 will correspond to riverwall_elevation[0]
        # The first index will correspond to riverwall_elevation[1]
        # etc
        #
        riverwallInds = (domain.edge_flux_type == 1).nonzero()[0]
        # elevation
        self.riverwall_elevation=\
            riverwall_elevation[riverwallInds]
        # corresponding row in the hydraulic properties table
        self.hydraulic_properties_rowIndex=\
            riverwall_rowIndex[riverwallInds].astype(int)
        # index of edges which are riverwalls
        self.riverwall_edges = riverwallInds

        # Record the names of the riverwalls
        self.names = nw_names

        # Now create the hydraulic properties table

        # Temporary variable to hold hydraulic properties table
        # This will have as many rows are there are distinct riverwalls,
        # and as many columns as there are hydraulic variables
        hydraulicTmp = numpy.zeros(
            (len(riverwalls), len(default_riverwallPar))) * numpy.nan

        if (verbose):
            print ' '
        # Loop over every riverwall / hydraulic parameter, and set its value
        for i in nw:
            # Get the riverwall's name and specified parameters
            name_riverwalli = nw_names[i]
            if (riverwallPar.has_key(name_riverwalli)):
                riverwalli_Par = riverwallPar[name_riverwalli]
            else:
                riverwalli_Par = None

            # Set the ith riverwall's hydraulic properties
            for j, hydraulicVar in enumerate(self.hydraulic_variable_names):
                if ((riverwalli_Par is not None)
                        and (riverwalli_Par.has_key(hydraulicVar))):
                    if (verbose):
                        printInfo=printInfo+ '  Using provided '+ str(hydraulicVar)+' '+\
                           str(riverwalli_Par[hydraulicVar])+ ' for riverwall '+ str(name_riverwalli)+'\n'
                    hydraulicTmp[i, j] = riverwalli_Par[hydraulicVar]
                else:
                    if (verbose):
                        printInfo=printInfo+ '  Using default '+ str(hydraulicVar)+' '+\
                            str(default_riverwallPar[hydraulicVar])+' for riverwall '+ str(name_riverwalli)+'\n'
                    hydraulicTmp[i, j] = default_riverwallPar[hydraulicVar]

        if (verbose):
            print ' '

        # Check that s1 < s2
        for i in nw:
            if (hydraulicTmp[i, 1] >= hydraulicTmp[i, 2]):
                msg = 's1 >= s2 on riverwall ' + nw_names[
                    i] + '. This is not allowed'
                raise Exception, msg
            if ((hydraulicTmp[i, 1] < 0.) or (hydraulicTmp[i, 2] < 0.)):
                raise Exception, 's1 and s2 must be positive, with s1<s2'

        # Check that h1 < h2
        for i in nw:
            if (hydraulicTmp[i, 3] >= hydraulicTmp[i, 4]):
                msg = 'h1 >= h2 on riverwall ' + nw_names[
                    i] + '. This is not allowed'
                raise Exception, msg
            if ((hydraulicTmp[i, 3] < 0.) or (hydraulicTmp[i, 4] < 0.)):
                raise Exception, 'h1 and h2 must be positive, with h1<h2'

        # Define the hydraulic properties
        self.hydraulic_properties = hydraulicTmp

        # Check for riverwall 'connectedness' errors (e.g. theoretically possible
        # to miss an edge due to round-off)
        connectedness = self.check_riverwall_connectedness(verbose=verbose)

        self.export_riverwalls_to_text(output_dir=output_dir)

        # Pretty printing of riverwall information in parallel
        if (verbose):
            if domain.parallel: barrier()
            for i in range(numprocs):
                if (myid == i):
                    print 'Processor ' + str(myid)
                    print printInfo
                    print connectedness[0]
                    msg='Riverwall discontinuity -- possible round-off error in'+\
                         'finding edges on wall -- try increasing value of tol'
                    if (not connectedness[1]):
                        raise Exception, msg
                if domain.parallel: barrier()
        return
コード例 #9
0
                    verbose=True
                    )


    #--------------------------------------------------------------------------
    # Create the computational domain based on overall clipping polygon with
    # a tagged boundary and interior regions defined in project.py along with
    # resolutions (maximal area of per triangle) for each polygon
    #--------------------------------------------------------------------------

    log.critical('Create computational domain')

else:
    print 'Hello from processor ', myid

barrier()
    

# Read in boundary from ordered sts file
event_sts = anuga.create_sts_boundary(project.event_sts)

# Reading the landward defined points, this incorporates the original clipping
# polygon minus the 100m contour
landward_boundary = anuga.read_polygon(project.landward_boundary)

# Combine sts polyline with landward points
bounding_polygon_sts = event_sts + landward_boundary

# Number of boundary segments
num_ocean_segments = len(event_sts) - 1
# Number of landward_boundary points
コード例 #10
0
def run_simulation(parallel=False, verbose=False):

    #--------------------------------------------------------------------------
    # Setup computational domain and quantities
    #--------------------------------------------------------------------------
    if myid == 0:
        anuga.create_mesh_from_regions(boundaryPolygon, 
                                 boundary_tags={'left': [0],
                                                'top': [1],
                                                'right': [2],
                                                'bottom': [3]},
                                   maximum_triangle_area = 1.0e+20,
                                   minimum_triangle_angle = 28.0,
                                   filename = 'runup.msh',
                                   interior_regions = [ [higherResPolygon, 1.*1.*0.5],
                                                        [midResPolygon, 3.0*3.0*0.5]],
                                   breaklines=riverWall.values(),
                                   use_cache=False,
                                   verbose=verbose,
                                   regionPtArea=regionPtAreas)
        
        sdomain=anuga.create_domain_from_file('runup.msh')
        
        
        sdomain.set_flow_algorithm(alg)
        
        
        sdomain.set_name('s_riverwall')                         
        sdomain.set_datadir('.')                         
        sdomain.set_store_vertices_uniquely()
        
        #------------------
        # Define topography
        #------------------
        
        def topography(x,y):
            return -x/150.*scale_me 
        
        def stagefun(x,y):
            stg=-0.5*scale_me
            return stg 
        
        sdomain.set_quantity('elevation',topography)     # Use function for elevation
        sdomain.set_quantity('friction',0.03)             # Constant friction
        sdomain.set_quantity('stage', stagefun)              # Constant negative initial stage
    else:
        sdomain = None
        
    #--------------------------------------------------------------------------
    # Create the parallel domains
    #--------------------------------------------------------------------------
    if parallel:
        
        if myid == 0 and verbose : print 'DISTRIBUTING TO PARALLEL DOMAIN'
        pdomain = distribute(sdomain, verbose=verbose)
        pdomain.set_name('p_riverwall')
        pdomain.set_store_vertices_uniquely()
        
        
    if myid == 0 and verbose: 
        print 60*'='
        print 'EVOLVING pdomain'
        print 60*'='
            
    setup_and_evolve(pdomain, verbose=verbose)
 
    barrier()
   
    if myid == 0:
        if verbose: 
            print 60*'='
            print 'EVOLVING sdomain'
            print 60*'='  
        setup_and_evolve(sdomain, verbose=verbose)
      
    barrier()
    
    #---------------------------------
    # Now compare the merged sww files
    #---------------------------------
    if myid == 0:
        if verbose: print 'COMPARING SWW FILES'
        
        sdomain_v = util.get_output('s_riverwall.sww')
        sdomain_c = util.get_centroids(sdomain_v)

        pdomain_v = util.get_output('p_riverwall.sww')
        pdomain_c = util.get_centroids(pdomain_v)
        

        # Test some values against the original ordering
        
        if verbose:
            
            order = 0
            print 'PDOMAIN CENTROID VALUES'
            print num.linalg.norm(sdomain_c.x-pdomain_c.x,ord=order)
            print num.linalg.norm(sdomain_c.y-pdomain_c.y,ord=order)
            print num.linalg.norm(sdomain_c.stage[-1]-pdomain_c.stage[-1],ord=order)
            print num.linalg.norm(sdomain_c.xmom[-1]-pdomain_c.xmom[-1],ord=order)
            print num.linalg.norm(sdomain_c.ymom[-1]-pdomain_c.ymom[-1],ord=order)
            print num.linalg.norm(sdomain_c.xvel[-1]-pdomain_c.xvel[-1],ord=order)
            print num.linalg.norm(sdomain_c.yvel[-1]-pdomain_c.yvel[-1],ord=order)        
            
        assert num.allclose(sdomain_c.stage,pdomain_c.stage)
        assert num.allclose(sdomain_c.xmom,pdomain_c.xmom)
        assert num.allclose(sdomain_c.ymom,pdomain_c.ymom)
        assert num.allclose(sdomain_c.xvel,pdomain_c.xvel)
        assert num.allclose(sdomain_c.yvel,pdomain_c.yvel)
        
        assert num.allclose(sdomain_v.x,pdomain_v.x)
        assert num.allclose(sdomain_v.y,pdomain_v.y)
        
        
        import os
        os.remove('s_riverwall.sww')
        os.remove('p_riverwall.sww')
        os.remove('runup.msh')
コード例 #11
0
ファイル: riverwall.py プロジェクト: pabryan/anuga_core
    def export_riverwalls_to_text(self, output_dir=None):
        """
            Function for dumping riverwall outputs to text file (useful for QC)

            This will overwrite any existing files with the same location/name

            INPUT: output_dir = Directory where the outputs will be written

            OUTPUT:
                    None, but writes files as a side effect

        """
        if(output_dir is None):
            return
    
        if(myid == 0):
            # Make output directory
            try: 
                os.mkdir(output_dir)
            except:
                pass
            # Make output files with empty contents
            for i, riverWallFile in enumerate(self.names):
                newFile=open(output_dir + '/' + os.path.splitext(os.path.basename(riverWallFile))[0] + '.txt','w')
                # Write hydraulic variable information
                hydraulicVars=self.hydraulic_properties[i,:]
                newFile.write('## Hydraulic Variable values below ## \n')
                newFile.write(str(self.hydraulic_variable_names) + '\n')
                newFile.write(str(hydraulicVars) + '\n')
                newFile.write('\n')
                newFile.write('## xyElevation at edges below. Order may be erratic for parallel runs ##\n')
                newFile.close()
        else:
            pass
        



        domain = self.domain

        # The other processes might try to write into file
        # before process 0 has created file, so we need a 
        # barrier
        if domain.parallel: barrier()    

        # Now dump the required info to the files
        for i in range(numprocs):
            # Write 1 processor at a time
            if(myid == i):
                for j, riverWallname in enumerate(self.names):
                    # Get xyz data for riverwall j
                    riverWallInds = (self.hydraulic_properties_rowIndex==j).nonzero()[0].tolist()
                    riverWallDomainInds = self.riverwall_edges[riverWallInds].tolist()
                    myXCoords = domain.edge_coordinates[riverWallDomainInds,0] + domain.geo_reference.xllcorner
                    myYCoords = domain.edge_coordinates[riverWallDomainInds,1] + domain.geo_reference.yllcorner
                    myElev = self.riverwall_elevation[riverWallInds]
               
                    # Open file for appending data 
                    theFile = open(output_dir + '/' + os.path.splitext(os.path.basename(riverWallname))[0] + '.txt','a')
                    for k in range(len(myElev)):
                        theFile.write(str(myXCoords[k]) + ',' + str(myYCoords[k]) + ',' + str(myElev[k]) + '\n')
                    theFile.close()
                        
            else:
                pass
 

        return
コード例 #12
0
ファイル: riverwall.py プロジェクト: pabryan/anuga_core
    def create_riverwalls(self, riverwalls, riverwallPar={ },
                          default_riverwallPar={ },
                          tol=1.0e-4, verbose=True, 
                          output_dir=None):
        """Add riverwalls at chosen locations along the mesh

        As of 22/04/2014, these only work with DE algorithms [for which the concept is natural]

        The walls MUST EXACTLY COINCIDE with edges along the mesh 
        
        You can force the mesh to do this by passing riverwalls.values() 
        to the 'breaklines' argument in the function create_mesh_from_regions. You
        may also need to set the maximum_triangle_area for regions, if the breaklines
        split the region.  Do this with the regionPtArea argument in
        create_mesh_from_regions.

        As of 22/04/2014, the computational method used here is very 'brute-force'
        For each segment on each riverwall, every point in the mesh is checked to see
        if it is on the segment. A possibly faster/less memory method would be to
        'walk' through connected edges on the mesh.

        Inputs:
            riverwalls: Dictionary of '3D polygons', containing xyz locations of named riverwalls.

                exampleRiverWalls = { # Left bank n1 -- 
                                      'n1': [[1.0, 1000., 2.],
                                             [1.0, 50., 3.]],
                                      # Left bank n2 
                                       'n2': [[2.0, 30., 1.0],
                                              [3.0, 20., 2.], 
                                              [2.5, 15., 1.5]]
                                    }

            riverwallPar: Dictionary containing a dictionary of named hydraulic parameters for each named riverwall
                          If parameters are not provided, default values will be used. 
                          See the help for class 'RiverWall' for an explanation of these

                exampleRiverWallPar = {'n2': {'Qfactor':0.5} }
                    This would use a Qfactor of 0.5 for riverwall 'n2', while the other riverwall would have the default values

            default_riverwallPar:  Dictionary containing default values of the riverwall parameters, to be used
                                   if they are not explicitly set.
                                   If not provided, defaults from __init__ are used. See the help for class 'RiverWall' for more info

                example_default_riverwallPar = {'Qfactor':1.5,  
                                                's1': 0.9,      
                                                's2': 0.95,     
                                                'h1': 1.0,      
                                                'h2': 1.5       
                                               }

                example_default_riverwallPar = {'Qfactor':1.5,  
                                                's1': 10000.,      
                                                's2': 20000.     
                                               } # Here h1/h2 defaults will come from __init__
                 

            tol: Edges will be assigned a riverwall elevation if they are within 'tol' of
                 a segment in riverwalls. Round-off error means this should not be too small.

            verbose: TRUE/FALSE Print lots of information

            output_dir: Text representation of riverwalls is written to output_dir, unless output_dir=None

        Outputs:
            None, but it sets domain.edge_flux_type = 1 for every edge on a riverwall
            Also, it adds a RiverWall object domain.riverwallData to the domain
            The latter contains the riverwall heights, names, and hydraulic properties for each edge, in
              a way we can pass in/out of C code.

        """

        #if(verbose and myid==0):        
        #    print ' '
        #    print 'WARNING: Riverwall is an experimental feature'
        #    print '         At each riverwall edge, we place a thin "wall" between'
        #    print '         the 2 edges -- so each sees its neighbour edge as having'
        #    print '         bed elevation = max(levee height, neighbour bed elevation)'
        #    print '         We also force the discharge with a weir relation, blended with'
        #    print '         the shallow water flux solution as the ratio (min_head)/(weir_height) becomes '
        #    print '         large, or the ratio (downstream_head)/(upstream_head) becomes large'
        #    print ' '
        #    print '  It works in parallel, but you must use domain.riverwallData.create_riverwall AFTER distributing the mesh'
        #    print ' '

        # NOTE: domain.riverwallData is initialised in shallow_water_domain.py for DE algorithms
        domain=self.domain

        
        # Check flow algorithm
        if(not domain.get_using_discontinuous_elevation()):
            raise Exception, 'Riverwalls are currently only supported for discontinuous elevation flow algorithms'

        if(len(self.names)>0):
            # Delete any existing riverwall data
            # The function cannot presently be used to partially edit riverwall data
            if(verbose):
                print 'Warning: There seems to be existing riverwall data'
                print 'It will be deleted and overwritten with this function call'
            domain.riverwallData.__init__(domain)

        # Store input parameters
        # FIXME: Is this worth it?
        self.input_riverwall_geo=riverwalls
        self.input_riverwallPar=riverwallPar

        # Update self.default_riverwallPar (defined in __init__)
        for i in self.default_riverwallPar.keys():
            if(default_riverwallPar.has_key(i)):
                self.default_riverwallPar[i]=default_riverwallPar[i]

        # Check that all the keys in default_riverwallPar are allowed
        for i in default_riverwallPar.keys():
            if(not self.default_riverwallPar.has_key(i)):
                msg='Key ', i + ' in default_riverwallPar not recognized'
                raise Exception, msg
        # Final default river-wall parameters
        default_riverwallPar=self.default_riverwallPar
        
        # Check that all named inputs in riverwallPar correspond to names in
        # riverwall
        for i in riverwallPar.keys():
            if not riverwalls.has_key(i):
                msg= 'Key ', i, ' in riverwallPar has no corresponding key in riverwall'
                raise Exception, msg
            #
            # Check that all hydraulic parameter names in riverwallPar correspond
            # to names in default_riverwallPar
            #
            for j in riverwallPar[i].keys():
                if not default_riverwallPar.has_key(j):
                    msg = 'Hydraulic parameter named ', j ,\
                          ' not recognised in default_riverwallPar'
                    raise Exception, msg
        
        if(verbose):
            print 'Setting riverwall elevations (P'+str(myid)+')...'

        # Set up geometry
        exy=domain.edge_coordinates
        llx=domain.mesh.geo_reference.get_xllcorner()
        lly=domain.mesh.geo_reference.get_yllcorner()

        # Temporary variables
        from anuga.config import max_float
        riverwall_elevation=exy[:,0]*0. - max_float
        riverwall_Qfactor=exy[:,0]*0.
        riverwall_rowIndex=exy[:,0]*0 -1.
        riverwall_rowIndex.astype(int)

        # Loop over all segments in each riverwall, and set its elevation
        nw=range(len(riverwalls))
        nw_names=riverwalls.keys() # Not guarenteed to be in deterministic order

        if(verbose):
            # Use variable to record messages, allows cleaner parallel printing
            printInfo='' 

        for i in nw:
            # Name of riverwall
            riverwalli_name=nw_names[i]
            # Look at the ith riverwall
            riverwalli=riverwalls[riverwalli_name]

            ns=len(riverwalli)-1

            if(verbose): 
                printInfo=printInfo + '  Wall ' + str(i) +' ....\n'

            for j in range(ns):
                if(verbose):
                    printInfo=printInfo + '    Segment ' + str(j) +' ....\n'
                # Start and end xyz coordinates
                start=riverwalli[j]
                end=riverwalli[j+1]

                if(len(start)!=3 | len(end)!=3):
                    msg='Each riverwall coordinate must have at exactly 3 values [xyz]'
                    raise Exception, msg

                # Find length
                segLen=( (start[0]-end[0])**2+(start[1]-end[1])**2)**0.5
                if(segLen<tol):
                    if(verbose):
                        printInfo=printInfo+'  Segment with length < tolerance ' + str(tol) +' ignored\n'
                    continue 
                
                # Find edge indices which are within 'tol' of the segment
                # We use a simple, inefficient method [but likely ok in practice
                # except for very complex riverwalls]
                
                # Unit vector along segment
                se_0=-(start[0]-end[0])/segLen
                se_1=-(start[1]-end[1])/segLen

                # Vector from 'start' to every point on mesh
                # NOTE: We account for georeferencing
                pv_0 = exy[:,0]-(start[0]-llx)
                pv_1 = exy[:,1]-(start[1]-lly)

                pvLen=( pv_0**2 + pv_1**2)**0.5

                # Dot product of pv and se == along-segment distance of projection
                # of each point onto segment 
                pv_dot_se = pv_0*se_0+pv_1*se_1
                # Normal distance^2 of each point to segment
                perp_len_sq = pvLen**2.-pv_dot_se**2.
               
                # Point is on a levee if the perpendicular distance is < tol,
                # AND it is between start and end [within a tolerance]
                onLevee=(perp_len_sq<tol**2)*(pv_dot_se > 0.-tol)*(pv_dot_se<segLen+tol)
                onLevee=onLevee.nonzero()
                onLevee=onLevee[0]
                if(len(onLevee)==0):
                    continue

                if(verbose):
                    printInfo=printInfo+'       Finding ' + str(len(onLevee)) + ' edges on this segment\n'
            
                # Levee has Edge_flux_type=1  
                domain.edge_flux_type[onLevee]=1
     
                # Get edge elevations as weighted averages of start/end elevations 
                w0=pv_dot_se[onLevee]/segLen
                w0=w0*(w0>=0.0) # Enforce min of 0
                w0=w0*(w0<=1.0) + 1.0*(w0>1.0) # Max of 1
                riverwall_elevation[onLevee]= start[2]*(1.0-w0)+w0*end[2]

                # Record row index
                riverwall_rowIndex[onLevee] = i

        # Now, condense riverwall_elevation to array with length = number of riverwall edges
        #
        #  We do this to avoid storing a riverwall_elevation for every edge in the mesh
        #  However, the data structure ends up being quite complex -- maybe there is a better way?
        #
        # The zeroth index in domain.edge_flux_type which = 1 will correspond to riverwall_elevation[0]
        # The first index will correspond to riverwall_elevation[1]
        # etc
        #
        riverwallInds=(domain.edge_flux_type==1).nonzero()[0]
        # elevation
        self.riverwall_elevation=\
            riverwall_elevation[riverwallInds]
        # corresponding row in the hydraulic properties table
        self.hydraulic_properties_rowIndex=\
            riverwall_rowIndex[riverwallInds].astype(int)
        # index of edges which are riverwalls 
        self.riverwall_edges=riverwallInds

        # Record the names of the riverwalls
        self.names=nw_names

       
        # Now create the hydraulic properties table

        # Temporary variable to hold hydraulic properties table
        # This will have as many rows are there are distinct riverwalls,
        # and as many columns as there are hydraulic variables
        hydraulicTmp=numpy.zeros((len(riverwalls), len(default_riverwallPar)))*numpy.nan
       
        if(verbose):
            print ' ' 
        # Loop over every riverwall / hydraulic parameter, and set its value
        for i in nw:
            # Get the riverwall's name and specified parameters
            name_riverwalli=nw_names[i]
            if(riverwallPar.has_key(name_riverwalli)):
                riverwalli_Par=riverwallPar[name_riverwalli]
            else:
                riverwalli_Par=None

            # Set the ith riverwall's hydraulic properties 
            for j, hydraulicVar in enumerate(self.hydraulic_variable_names):    
                if((riverwalli_Par is not None) and (riverwalli_Par.has_key(hydraulicVar))):
                    if(verbose): 
                        printInfo=printInfo+ '  Using provided '+ str(hydraulicVar)+' '+\
                           str(riverwalli_Par[hydraulicVar])+ ' for riverwall '+ str(name_riverwalli)+'\n'
                    hydraulicTmp[i,j]=riverwalli_Par[hydraulicVar] 
                else:
                    if(verbose): 
                        printInfo=printInfo+ '  Using default '+ str(hydraulicVar)+' '+\
                            str(default_riverwallPar[hydraulicVar])+' for riverwall '+ str(name_riverwalli)+'\n'
                    hydraulicTmp[i,j]=default_riverwallPar[hydraulicVar]

        if(verbose):
            print ' '

        # Check that s1 < s2 
        for i in nw:
            if(hydraulicTmp[i,1]>= hydraulicTmp[i,2]):
                msg = 's1 >= s2 on riverwall ' + nw_names[i] +'. This is not allowed' 
                raise Exception, msg
            if( (hydraulicTmp[i,1]<0.) or (hydraulicTmp[i,2] < 0.)):
                raise Exception, 's1 and s2 must be positive, with s1<s2'

        # Check that h1 < h2
        for i in nw:
            if(hydraulicTmp[i,3]>= hydraulicTmp[i,4]):
                msg = 'h1 >= h2 on riverwall ' + nw_names[i] +'. This is not allowed' 
                raise Exception, msg
            if((hydraulicTmp[i,3]<0.) or (hydraulicTmp[i,4] < 0.)):
                raise Exception, 'h1 and h2 must be positive, with h1<h2'
       
        # Define the hydraulic properties 
        self.hydraulic_properties=hydraulicTmp
      
        # Check for riverwall 'connectedness' errors (e.g. theoretically possible
        # to miss an edge due to round-off)
        connectedness=self.check_riverwall_connectedness(verbose=verbose)

        self.export_riverwalls_to_text(output_dir=output_dir)
        
        # Pretty printing of riverwall information in parallel
        if(verbose): 
            if domain.parallel : barrier()
            for i in range(numprocs):
                if(myid==i):
                    print 'Processor '+str(myid)
                    print printInfo
                    print connectedness[0]
                    msg='Riverwall discontinuity -- possible round-off error in'+\
                         'finding edges on wall -- try increasing value of tol'
                    if(not connectedness[1]):
                        raise Exception, msg
                if domain.parallel : barrier()
        return 
コード例 #13
0
def start_sim(run_id, Runs, scenario_name, Scenario, session, **kwargs):
    yieldstep = kwargs['yieldstep']
    finaltime = kwargs['finaltime']
    logger = logging.getLogger(run_id)
    max_triangle_area = kwargs['max_triangle_area']
    logger.info('Starting hydrata_project')

    if run_id == 'local_run':
        base_dir = os.getcwd()
    else:
        base_dir = os.getcwd() + '/base_dir/%s/' % run_id

    outname = run_id
    meshname = base_dir + 'outputs/' + run_id + '.msh'

    def get_filename(data_type, file_type):
        files = os.listdir('%sinputs/%s' % (base_dir, data_type))
        filename = '%sinputs/%s/%s' % (
            base_dir, data_type, [f for f in files if f[-4:] == file_type][0])
        return filename

    boundary_data_filename = get_filename('boundary_data', '.shp')
    elevation_data_filename = get_filename('elevation_data', '.tif')
    try:
        structures_filename = get_filename('structures', '.shp')
    except OSError as e:
        structures_filename = None
    try:
        rain_data_filename = get_filename('rain_data', '.shp')
    except OSError as e:
        rain_data_filename = None
    try:
        inflow_data_filename = get_filename('inflow_data', '.shp')
    except OSError as e:
        inflow_data_filename = None
    try:
        friction_data_filename = get_filename('friction_data', '.shp')
    except OSError as e:
        friction_data_filename = None

    logger.info('boundary_data_filename: %s' % boundary_data_filename)
    logger.info('structures_filename: %s' % structures_filename)
    logger.info('rain_data_filename: %s' % rain_data_filename)
    logger.info('inflow_data_filename: %s' % inflow_data_filename)
    logger.info('friction_data_filename: %s' % friction_data_filename)
    logger.info('elevation_data_filename: %s' % elevation_data_filename)

    # create a list of project files
    vector_filenames = [
        boundary_data_filename, structures_filename, rain_data_filename,
        inflow_data_filename, friction_data_filename
    ]

    # set the projection system for ANUGA calculations from the geotiff elevation data
    elevation_data_gdal = gdal.Open(elevation_data_filename)
    project_spatial_ref = osr.SpatialReference()
    project_spatial_ref.ImportFromWkt(elevation_data_gdal.GetProjectionRef())
    project_spatial_ref_epsg_code = int(
        project_spatial_ref.GetAttrValue("AUTHORITY", 1))

    # check the spatial reference system of the project files matches that of the calculation
    for filename in vector_filenames:
        if filename:
            prj_text = open(filename[:-4] + '.prj').read()
            srs = osr.SpatialReference()
            srs.ImportFromESRI([prj_text])
            srs.AutoIdentifyEPSG()
            logger.info('filename is: %s' % filename)
            logger.info('EPSG is: %s' % srs.GetAuthorityCode(None))
            if str(srs.GetAuthorityCode(None)) != str(
                    project_spatial_ref_epsg_code):
                logger.warning('warning spatial refs are not maching: %s, %s' %
                               (srs.GetAuthorityCode(None),
                                project_spatial_ref_epsg_code))

    logger.info('Setting up structures...')
    if structures_filename:
        structures = []
        logger.info('processing structures from :%s' % structures_filename)
        ogr_shapefile = ogr.Open(structures_filename)
        ogr_layer = ogr_shapefile.GetLayer(0)
        ogr_layer_feature = ogr_layer.GetNextFeature()
        while ogr_layer_feature:
            structure = json.loads(ogr_layer_feature.GetGeometryRef().
                                   ExportToJson())['coordinates'][0]
            structures.append(structure)
            ogr_layer_feature = None
            ogr_layer_feature = ogr_layer.GetNextFeature()

        logger.info('structures: %s' % structures)
    else:
        logger.warning('warning: no structures found.')
        structures = None

    logger.info('Setting up friction...')
    frictions = []
    if friction_data_filename:
        logger.info('processing frictions from :%s' % friction_data_filename)
        ogr_shapefile = ogr.Open(friction_data_filename)
        ogr_layer = ogr_shapefile.GetLayer(0)
        ogr_layer_feature = ogr_layer.GetNextFeature()
        while ogr_layer_feature:
            friction_poly = json.loads(ogr_layer_feature.GetGeometryRef().
                                       ExportToJson())['coordinates'][0]
            friction_value = float(ogr_layer_feature.GetField('mannings'))
            friction_couple = [friction_poly, friction_value]
            frictions.append(friction_couple)
            ogr_layer_feature = None
            ogr_layer_feature = ogr_layer.GetNextFeature()

        frictions.append(['All', 0.04])
        logger.info('frictions: %s' % frictions)
    else:
        frictions.append(['All', 0.04])
        logger.info('warning: no frictions found.')

    logger.info('Setting up boundary conditions...')
    ogr_shapefile = ogr.Open(boundary_data_filename)
    ogr_layer = ogr_shapefile.GetLayer(0)
    ogr_layer_definition = ogr_layer.GetLayerDefn()
    logger.info('ogr_layer_definition.GetGeomType: %s' %
                ogr_layer_definition.GetGeomType())
    boundary_tag_index = 0
    bdy_tags = {}
    bdy = {}

    ogr_layer_feature = ogr_layer.GetNextFeature()
    while ogr_layer_feature:
        boundary_tag_key = ogr_layer_feature.GetField('bdy_tag_k')
        boundary_tag_value = ogr_layer_feature.GetField('bdy_tag_v')
        bdy_tags[boundary_tag_key] = [
            boundary_tag_index * 2, boundary_tag_index * 2 + 1
        ]
        bdy[boundary_tag_key] = boundary_tag_value
        geom = ogr_layer_feature.GetGeometryRef().GetPoints()
        ogr_layer_feature = None
        ogr_layer_feature = ogr_layer.GetNextFeature()
        boundary_tag_index = boundary_tag_index + 1
        logger.info('bdy_tags: %s' % bdy_tags)
    logger.info('bdy: %s' % bdy)

    boundary_data = su.read_polygon(boundary_data_filename)

    create_mesh_from_regions(boundary_data,
                             boundary_tags=bdy_tags,
                             maximum_triangle_area=max_triangle_area,
                             interior_regions=None,
                             interior_holes=structures,
                             filename=meshname,
                             use_cache=False,
                             verbose=True)

    domain = Domain(meshname, use_cache=False, verbose=True)
    domain.set_name(outname)
    domain.set_datadir(base_dir + '/outputs')
    logger.info(domain.statistics())
    poly_fun_pairs = [['Extent', elevation_data_filename.encode("utf-8")]]
    topography_function = qs.composite_quantity_setting_function(
        poly_fun_pairs,
        domain,
        nan_treatment='exception',
    )
    friction_function = qs.composite_quantity_setting_function(
        frictions, domain)
    domain.set_quantity('friction', friction_function, verbose=True)
    domain.set_quantity('stage', 0.0)
    domain.set_quantity('elevation',
                        topography_function,
                        verbose=True,
                        alpha=0.99)
    domain.set_minimum_storable_height(0.005)

    logger.info('Applying rainfall...')
    if rain_data_filename:
        ogr_shapefile = ogr.Open(rain_data_filename)
        ogr_layer = ogr_shapefile.GetLayer(0)
        rainfall = 0
        ogr_layer_feature = ogr_layer.GetNextFeature()
        while ogr_layer_feature:
            rainfall = float(ogr_layer_feature.GetField('rate_mm_hr'))
            polygon = su.read_polygon(rain_data_filename)
            logger.info("applying Polygonal_rate_operator with rate, polygon:")
            logger.info(rainfall)
            logger.info(polygon)
            Polygonal_rate_operator(domain,
                                    rate=rainfall,
                                    factor=1.0e-6,
                                    polygon=polygon,
                                    default_rate=0.0)
            ogr_layer_feature = None
            ogr_layer_feature = ogr_layer.GetNextFeature()

    logger.info('Applying surface inflows...')
    if inflow_data_filename:
        ogr_shapefile = ogr.Open(inflow_data_filename)
        ogr_layer = ogr_shapefile.GetLayer(0)
        ogr_layer_definition = ogr_layer.GetLayerDefn()
        ogr_layer_feature = ogr_layer.GetNextFeature()
        while ogr_layer_feature:
            in_fixed = float(ogr_layer_feature.GetField('in_fixed'))
            line = ogr_layer_feature.GetGeometryRef().GetPoints()
            logger.info("applying Inlet_operator with line, in_fixed:")
            logger.info(line)
            logger.info(in_fixed)
            Inlet_operator(domain, line, in_fixed, verbose=False)
            ogr_layer_feature = None
            ogr_layer_feature = ogr_layer.GetNextFeature()

    logger.info('Applying Boundary Conditions...')
    logger.info('Available boundary tags: %s' % domain.get_boundary_tags())

    Br = anuga.Reflective_boundary(domain)
    Bd = anuga.Dirichlet_boundary([0.0, 0.0, 0.0])
    Bt = anuga.Transmissive_boundary(domain)

    for key, value in bdy.iteritems():
        if value == 'Br':
            bdy[key] = Br
        elif value == 'Bd':
            bdy[key] = Bd
        elif value == 'Bt':
            bdy[key] = Bt
        else:
            logger.info(
                'No matching boundary condition exists - please check your shapefile attributes in: %s'
                % boundary_data_filename)

    # set a default value for exterior & interior boundary if it is not already set
    try:
        bdy['exterior']
    except KeyError:
        bdy['exterior'] = Br
    try:
        bdy['interior']
    except KeyError:
        bdy['interior'] = Br

    logger.info('bdy: %s' % bdy)

    domain.set_boundary(bdy)

    domain = distribute(domain)
    logger.info('Beginning evolve phase...')
    for t in domain.evolve(yieldstep, finaltime):
        domain.write_time()
        print domain.timestepping_statistics()
        logger.info(domain.timestepping_statistics(track_speeds=True))
        percentage_complete = round(domain.time / domain.finaltime, 3) * 100
        logger.info('%s percent complete' % percentage_complete)
        if run_id != 'local_run':
            write_percentage_complete(run_id, Runs, scenario_name, Scenario,
                                      session, percentage_complete)
    domain.sww_merge(delete_old=True)
    barrier()
    finalize()
    sww_file = base_dir + '/outputs/' + run_id + '.sww'
    sww_file = sww_file.encode(
        'utf-8',
        'ignore')  # sometimes run_id gets turned to a unicode object by celery
    util.Make_Geotif(swwFile=sww_file,
                     output_quantities=['depth', 'velocity'],
                     myTimeStep='max',
                     CellSize=max_triangle_area,
                     lower_left=None,
                     upper_right=None,
                     EPSG_CODE=project_spatial_ref_epsg_code,
                     proj4string=None,
                     velocity_extrapolation=True,
                     min_allowed_height=1.0e-05,
                     output_dir=(base_dir + '/outputs/'),
                     bounding_polygon=boundary_data,
                     internal_holes=structures,
                     verbose=False,
                     k_nearest_neighbours=3,
                     creation_options=[])
    logger.info("Done. Nice work.")
コード例 #14
0
def run_simulation(parallel=False, verbose=False):

    #--------------------------------------------------------------------------
    # Setup computational domain and quantities
    #--------------------------------------------------------------------------
    if myid == 0:
        anuga.create_mesh_from_regions(
            boundaryPolygon,
            boundary_tags={
                'left': [0],
                'top': [1],
                'right': [2],
                'bottom': [3]
            },
            maximum_triangle_area=1.0e+20,
            minimum_triangle_angle=28.0,
            filename='runup.msh',
            interior_regions=[[higherResPolygon, 1. * 1. * 0.5],
                              [midResPolygon, 3.0 * 3.0 * 0.5]],
            breaklines=list(riverWall.values()),
            use_cache=False,
            verbose=verbose,
            regionPtArea=regionPtAreas)

        sdomain = anuga.create_domain_from_file('runup.msh')

        sdomain.set_flow_algorithm(alg)

        sdomain.set_name('s_riverwall')
        sdomain.set_datadir('.')
        sdomain.set_store_vertices_uniquely()

        #------------------
        # Define topography
        #------------------

        def topography(x, y):
            return -x / 150. * scale_me

        def stagefun(x, y):
            stg = -0.5 * scale_me
            return stg

        sdomain.set_quantity('elevation',
                             topography)  # Use function for elevation
        sdomain.set_quantity('friction', 0.03)  # Constant friction
        sdomain.set_quantity('stage',
                             stagefun)  # Constant negative initial stage
    else:
        sdomain = None

    #--------------------------------------------------------------------------
    # Create the parallel domains
    #--------------------------------------------------------------------------
    if parallel:

        if myid == 0 and verbose: print('DISTRIBUTING TO PARALLEL DOMAIN')
        pdomain = distribute(sdomain, verbose=verbose)
        pdomain.set_name('p_riverwall')
        pdomain.set_store_vertices_uniquely()

    if myid == 0 and verbose:
        print(60 * '=')
        print('EVOLVING pdomain')
        print(60 * '=')

    setup_and_evolve(pdomain, verbose=verbose)

    barrier()

    if myid == 0:
        if verbose:
            print(60 * '=')
            print('EVOLVING sdomain')
            print(60 * '=')
        setup_and_evolve(sdomain, verbose=verbose)

    barrier()

    #---------------------------------
    # Now compare the merged sww files
    #---------------------------------
    if myid == 0:
        if verbose: print('COMPARING SWW FILES')

        sdomain_v = util.get_output('s_riverwall.sww')
        sdomain_c = util.get_centroids(sdomain_v)

        pdomain_v = util.get_output('p_riverwall.sww')
        pdomain_c = util.get_centroids(pdomain_v)

        # Test some values against the original ordering

        if verbose:

            order = 0
            print('PDOMAIN CENTROID VALUES')
            print(num.linalg.norm(sdomain_c.x - pdomain_c.x, ord=order))
            print(num.linalg.norm(sdomain_c.y - pdomain_c.y, ord=order))
            print(
                num.linalg.norm(sdomain_c.stage[-1] - pdomain_c.stage[-1],
                                ord=order))
            print(
                num.linalg.norm(sdomain_c.xmom[-1] - pdomain_c.xmom[-1],
                                ord=order))
            print(
                num.linalg.norm(sdomain_c.ymom[-1] - pdomain_c.ymom[-1],
                                ord=order))
            print(
                num.linalg.norm(sdomain_c.xvel[-1] - pdomain_c.xvel[-1],
                                ord=order))
            print(
                num.linalg.norm(sdomain_c.yvel[-1] - pdomain_c.yvel[-1],
                                ord=order))

        assert num.allclose(sdomain_c.stage, pdomain_c.stage)
        assert num.allclose(sdomain_c.xmom, pdomain_c.xmom)
        assert num.allclose(sdomain_c.ymom, pdomain_c.ymom)
        assert num.allclose(sdomain_c.xvel, pdomain_c.xvel)
        assert num.allclose(sdomain_c.yvel, pdomain_c.yvel)

        assert num.allclose(sdomain_v.x, pdomain_v.x)
        assert num.allclose(sdomain_v.y, pdomain_v.y)

        import os
        os.remove('s_riverwall.sww')
        os.remove('p_riverwall.sww')
        os.remove('runup.msh')
コード例 #15
0
# setup and create operator within polys setting the scour base elevations for each poly
op0 = Sanddune_erosion_operator(domain, base=nsbase_elev_c, indices=indices_union, Ra=45)  # both dunes
# op1 = sanddune_erosion_operator(domain, base=nsbase_elev_c, polygon=polygon1)   # first notched dune
# op2 = sanddune_erosion_operator(domain, base=nsbase_elev_c, polygon=polygon2)   # second plain dune


# ------------------------------------------------------------------------------
# Evolve sanddune erosion simulation through time
# ------------------------------------------------------------------------------
for t in domain.evolve(yieldstep=1, duration=600.0):
    if myid == 0:
        domain.print_timestepping_statistics()


#  run completed - tidy up
barrier()
if myid == 0:
    print " >>>>> Simulation completed succesfully "
    print " >>>>> Merging the individual cpu sww files and deleting the individual swws once merged"

# Merge the individual parallel swws created by the n processors
barrier()  # wait foir all processors to complete
domain.sww_merge(delete_old=False)

if myid == 0:
    print " >>>>> Finalising the run -- all done"

# Finaise the parallel code and this model run
barrier()  # wait for all processors to complete
finalize()
コード例 #16
0
def distibute_three_processors():
    """
    Do a parallel test of distributing a rectangle onto 3 processors

    """

    # FIXME: Need to update expected values on macos
    if sys.platform == 'darwin':
        return

    # FIXME: Need to update expected values on macos
    #if sys.platform == 'win32':
    #	return

    from anuga.utilities import parallel_abstraction as pypar

    myid = pypar.rank()
    numprocs = pypar.size()

    if not numprocs == 3:
        return

    try:
        import pymetis
        metis_version = 5
    except:
        metis_version = 4

    #print numprocs

    #barrier()

    if myid == 0:

        nodes_0, triangles_0, boundary_0 = rectangular_cross(2, 2)

        domain = Domain(nodes_0, triangles_0, boundary_0)

        domain.set_quantity('elevation',
                            topography)  # Use function for elevation
        domain.set_quantity('friction', 0.0)  # Constant friction
        domain.set_quantity('stage',
                            expression='elevation')  # Dry initial stage
        domain.set_quantity('xmomentum', expression='friction + 2.0')
        domain.set_quantity('ymomentum', ycoord)

        #----------------------------------------------------------------------------------
        # Test pmesh_divide_metis
        #----------------------------------------------------------------------------------
        vertices, triangles, boundary, triangles_per_proc, quantities = pmesh_divide_metis(
            domain, numprocs)

        if False:
            print_seq_values(vertices, triangles, triangles_per_proc)

        true_seq_values = get_true_seq_values(metis_version=metis_version)

        if False:
            print("True Seq Values = \\")
            pprint(true_seq_values)

        assert_allclose(vertices, true_seq_values['vertices'])
        assert_allclose(triangles, true_seq_values['triangles'])
        assert_allclose(triangles_per_proc,
                        true_seq_values['triangles_per_proc'])

        #----------------------------------------------------------------------------------
        # Test build_submesh
        #----------------------------------------------------------------------------------
        submesh = build_submesh(vertices, triangles, boundary, quantities,
                                triangles_per_proc)

        if False:
            print('submesh_values = \\')
            print_submesh_values(submesh)

        true_values = get_true_submesh_values(metis_version)

        assert_allclose(submesh['full_nodes'][0], true_values['full_nodes_0'])
        assert_allclose(submesh['full_nodes'][1], true_values['full_nodes_1'])
        assert_allclose(submesh['full_nodes'][2], true_values['full_nodes_2'])

        assert_allclose(submesh['ghost_nodes'][0],
                        true_values['ghost_nodes_0'])
        assert_allclose(submesh['ghost_nodes'][1],
                        true_values['ghost_nodes_1'])
        assert_allclose(submesh['ghost_nodes'][2],
                        true_values['ghost_nodes_2'])

        assert_allclose(submesh['full_triangles'][0],
                        true_values['full_triangles_0'])
        assert_allclose(submesh['full_triangles'][1],
                        true_values['full_triangles_1'])
        assert_allclose(submesh['full_triangles'][2],
                        true_values['full_triangles_2'])

        assert_allclose(submesh['ghost_triangles'][0],
                        true_values['ghost_triangles_0'])
        assert_allclose(submesh['ghost_triangles'][1],
                        true_values['ghost_triangles_1'])
        assert_allclose(submesh['ghost_triangles'][2],
                        true_values['ghost_triangles_2'])

        assert_allclose(submesh['ghost_commun'][0],
                        true_values['ghost_commun_0'])
        assert_allclose(submesh['ghost_commun'][1],
                        true_values['ghost_commun_1'])
        assert_allclose(submesh['ghost_commun'][2],
                        true_values['ghost_commun_2'])

        assert_(submesh['full_commun'] == true_values['full_commun'])

    barrier()
    #--------------------------------
    # Now do the comunnication part
    #--------------------------------

    if myid == 0:

        points, vertices, boundary, quantities, \
                    ghost_recv_dict, full_send_dict, tri_map, node_map, tri_l2g, node_l2g, \
                    ghost_layer_width =\
                    extract_submesh(submesh, triangles_per_proc)

        #----------------------------------------------------------------------------------
        # Test send_submesh
        #----------------------------------------------------------------------------------
        for p in range(1, numprocs):
            send_submesh(submesh, triangles_per_proc, p, verbose=False)
    else:
        #----------------------------------------------------------------------------------
        # Test rec_submesh
        #----------------------------------------------------------------------------------
        points, triangles, boundary, quantities, \
                ghost_recv_dict, full_send_dict, \
                no_full_nodes, no_full_trigs, tri_map, node_map, tri_l2g, node_l2g, \
                ghost_layer_width = \
                rec_submesh(0, verbose=False)

    barrier()

    #--------------------------------
    # Now do the test
    #--------------------------------
    if myid == 0:

        if False:
            print('extract_values = \\')
            print_extract_submesh(points, triangles, ghost_recv_dict, \
                                  full_send_dict, tri_map, node_map, ghost_layer_width)

        true_values = get_true_extract_submesh(metis_version)

        assert_allclose(points, true_values['points'])
        assert_allclose(triangles, true_values['triangles'])
        assert_allclose(ghost_recv_dict[1], true_values['ghost_recv_dict_1'])
        assert_allclose(ghost_recv_dict[2], true_values['ghost_recv_dict_2'])
        assert_allclose(full_send_dict[1], true_values['full_send_dict_1'])
        assert_allclose(full_send_dict[2], true_values['full_send_dict_2'])
        assert_allclose(tri_map, true_values['tri_map'])
        assert_allclose(node_map, true_values['node_map'])
        assert_allclose(ghost_layer_width, true_values['ghost_layer_width'])

    if myid == 1:

        if False:
            print("rec_submesh_1 = \\")
            print_rec_submesh_1(points, triangles, ghost_recv_dict, full_send_dict, \
                         tri_map, node_map, ghost_layer_width)

        true_values = get_true_rec_submesh_1(metis_version)

        if False:
            print('true_rec_values_1 = \\')
            pprint(true_values)

        assert_allclose(points, true_values['points'])
        assert_allclose(triangles, true_values['triangles'])
        assert_allclose(ghost_recv_dict[0], true_values['ghost_recv_dict_0'])
        assert_allclose(ghost_recv_dict[2], true_values['ghost_recv_dict_2'])
        assert_allclose(full_send_dict[0], true_values['full_send_dict_0'])
        assert_allclose(full_send_dict[2], true_values['full_send_dict_2'])
        assert_allclose(tri_map, true_values['tri_map'])
        assert_allclose(node_map, true_values['node_map'])
        assert_allclose(ghost_layer_width, true_values['ghost_layer_width'])

    if myid == 2:

        if False:
            print("rec_submesh_2 = \\")
            print_rec_submesh_2(points, triangles, ghost_recv_dict, full_send_dict, \
                         tri_map, node_map, ghost_layer_width)

        true_values = get_true_rec_submesh_2(metis_version)

        if False:
            print('true_rec_values_2 = \\')
            pprint(true_values)

        assert_allclose(points, true_values['points'])
        assert_allclose(triangles, true_values['triangles'])
        assert_allclose(ghost_recv_dict[0], true_values['ghost_recv_dict_0'])
        assert_allclose(ghost_recv_dict[1], true_values['ghost_recv_dict_1'])
        assert_allclose(full_send_dict[0], true_values['full_send_dict_0'])
        assert_allclose(full_send_dict[1], true_values['full_send_dict_1'])
        assert_allclose(tri_map, true_values['tri_map'])
        assert_allclose(node_map, true_values['node_map'])
        assert_allclose(ghost_layer_width, true_values['ghost_layer_width'])

    finalize()
コード例 #17
0
# setup and create operator within polys setting the scour base elevations for each poly
op0 = Sanddune_erosion_operator(domain,
                                base=nsbase_elev_c,
                                indices=indices_union,
                                Ra=45)  # both dunes
#op1 = sanddune_erosion_operator(domain, base=nsbase_elev_c, polygon=polygon1)   # first notched dune
#op2 = sanddune_erosion_operator(domain, base=nsbase_elev_c, polygon=polygon2)   # second plain dune

#------------------------------------------------------------------------------
# Evolve sanddune erosion simulation through time
#------------------------------------------------------------------------------
for t in domain.evolve(yieldstep=1, duration=600.0):
    if myid == 0: domain.print_timestepping_statistics()

#  run completed - tidy up
barrier()
if myid == 0:
    print ' >>>>> Simulation completed succesfully '
    print ' >>>>> Merging the individual cpu sww files and deleting the individual swws once merged'

# Merge the individual parallel swws created by the n processors
barrier()  # wait foir all processors to complete
domain.sww_merge(delete_old=False)

if myid == 0:
    print ' >>>>> Finalising the run -- all done'

# Finaise the parallel code and this model run
barrier()  # wait for all processors to complete
finalize()
コード例 #18
0
                                      len2=width)

    domain.set_quantity('elevation', -1.0)
    domain.set_quantity('stage', Set_Stage(h=2.0))
else:
    domain = None

#--------------------------------------------------------------------------
# Distribute sequential domain on processor 0 to other processors
#--------------------------------------------------------------------------

if myid == 0 and verbose: print('DISTRIBUTING DOMAIN')
domain = distribute(domain)

#domain.smooth = False
barrier()
for p in range(numprocs):
    if myid == p:
        print('Process ID %g' % myid)
        print('Number of triangles %g ' % domain.get_number_of_triangles())
        sys.stdout.flush()

    barrier()

domain.set_flow_algorithm(2.0)

if myid == 0:
    domain.print_algorithm_parameters()
    sys.stdout.flush()

barrier()