Index: /anuga_validation/uq_friction_2007/calc_norm.py
===================================================================
--- /anuga_validation/uq_friction_2007/calc_norm.py	(revision 4895)
+++ /anuga_validation/uq_friction_2007/calc_norm.py	(revision 4895)
@@ -0,0 +1,135 @@
+"""
+Idea's
+have it use cache!
+"""
+
+
+#----------------------------------------------------------------------------
+# Import necessary modules
+#----------------------------------------------------------------------------
+
+# Standard modules
+import os
+from os import sep, path
+import csv
+
+# Related major packages
+import project              
+from anuga.abstract_2d_finite_volumes.util import file_function
+from numerical_tools import  err   # norm, corr,  
+#X:\anuga_core\source\anuga\utilities\numerical_tools import  err 
+
+def load_csv(file_name):
+    """
+    Load in the csv as a dic, title as key and column info as value, .
+    Also, create a dic, title as key and column index as value,
+    to keep track of the column order. 
+    """
+    #
+    attribute_dic = {}
+    title_index_dic = {}
+    titles_stripped = [] # list of titles
+    
+    reader = csv.reader(file(file_name))
+
+    # Read in and manipulate the title info
+    titles = reader.next()
+    for i,title in enumerate(titles):
+        titles_stripped.append(title.strip())
+        title_index_dic[title.strip()] = i
+    title_count = len(titles_stripped)       
+    #print "title_index_dic",title_index_dic
+
+    
+    #create a dic of colum values, indexed by column title
+    for line in reader:
+        if len(line) <> title_count:
+            raise IOError #FIXME make this nicer
+        for i, value in enumerate(line):
+            attribute_dic.setdefault(titles_stripped[i],[]).append(value)
+        
+    return attribute_dic, title_index_dic
+
+
+def write_norm_results( file_name, norms):
+    fd = open(file_name, 'w')
+    fd.write( 'sww_file, friction, 2nd normal' + '\n')
+    for norm in norms:
+        fd.write(norm[0] + ', ' + str(norm[1]) + ', ' + str(norm[2]) + '\n')
+    fd.close()    
+    
+def calc_norm(flume_name,
+              is_trial_run=False,
+              outputdir_name=None,
+              pro_instance=None):    
+    if is_trial_run is True:
+        outputdir_name += '_test'
+    if pro_instance is None:
+        pro_instance = project.Project(['data','flumes','dam_2006'],
+                                       outputdir_name=outputdir_name)
+    
+    
+    #  Read in the flume data
+    flume_results = path.join(pro_instance.home, 'data', 'flumes',
+                              'dam_UQ_data_2006', 'longer_data',
+                              flume_name)
+    flume_results, _ = load_csv(flume_results)
+    #print "flume_results",flume_results #.keys()
+
+    #print "flume_results['time']", flume_results['time']
+    #Get a list of the files
+    files = os.listdir(pro_instance.outputdir)
+    files = [x for x in files if x[-4:] == '.sww']
+    files.sort()
+    print "checking against files: ",files 
+
+    quantities = ['stage', 'elevation']
+    gauge_locations =  [[0.2, 0.2],
+                        [0.3, 0.2],
+                        [0.4, 0.2],
+                        [0.5, 0.2],
+                        [0.6, 0.2]]
+
+    norm_sums = []
+    for sww_file in files:
+        #print "sww_file",sww_file 
+        file_instance = file_function(pro_instance.outputdir + sep + sww_file,
+				      quantities = quantities,
+				      interpolation_points = gauge_locations,
+				      verbose = True,
+				      use_cache = True)
+        # file_instance(0.02, point_id=0) #This works
+        norm_sum = 0
+        for location in range(len(gauge_locations)):
+	    #print "location",location
+	    #print " gauge_locations[location]", gauge_locations[location]
+            simulated_depths = []
+            #print "flume_results['time']",flume_results['time'] 
+            for time in flume_results['time']:
+                quantities_slice = file_instance(float(time),
+						 point_id=location)
+                #print "quantities", quantities_slice 
+                depth = quantities_slice[0] - quantities_slice[1]
+                simulated_depths.append(depth)
+            #print "simulated_depths",simulated_depths 
+	    # get the flume depth at this location
+	    flume_depths = flume_results[str(gauge_locations[location][0])]
+            flume_depths = [float(i) for i in flume_depths]
+	    # calc the norm
+            #print "map(None, simulated_depths, flume_depths)", \
+            #      map(None, simulated_depths, flume_depths)
+	    norm = err(simulated_depths,
+	    	       flume_depths, 2, relative = True)  # 2nd norm (rel. RMS)
+            norm_sum += norm
+        print "norm_sum",norm_sum
+        norm_sums.append([sww_file, sww_file[2:-4], norm_sum])
+        norm_file_name = pro_instance.outputdir + sep + \
+                           flume_name[:-4]+'_norm' + flume_name[-4:]
+        write_norm_results(norm_file_name, norm_sums)
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    calc_norm('fromD_0.2_Slope0.05_x0.2-0.6_clean.csv',
+              is_trial_run = False,
+              outputdir_name='friction_set_A')
+    
Index: /anuga_validation/uq_friction_2007/create_mesh.py
===================================================================
--- /anuga_validation/uq_friction_2007/create_mesh.py	(revision 4895)
+++ /anuga_validation/uq_friction_2007/create_mesh.py	(revision 4895)
@@ -0,0 +1,67 @@
+"""Create mesh for University of Queensland dam break flume
+"""
+
+
+from anuga.pmesh.mesh import *
+from anuga.coordinate_transforms.geo_reference import Geo_reference
+
+
+def generate(mesh_filename, gate_position, is_coarse = False):
+    """
+    Generate mesh for University of Queensland dam break flume.
+    The gate position is the distance from the right wall of the wave tank
+    to the gate. 
+    
+    """
+    #Basic geometry
+    
+    xright  = gate_position 
+    ybottom = 0
+    ytop    = 0.4
+    xdam = 0.0
+    xleft = gate_position  - 3.0
+
+    #Outline 
+    point_sw = [xleft, ybottom]
+    point_se = [xright, ybottom]
+    point_nw = [xleft, ytop]    
+    point_ne = [xright, ytop]
+
+    # Dam seperation (left)
+    point_dam_top = [xdam, ytop]
+    point_dam_bottom = [xdam, ybottom]    
+
+    m = Mesh()
+
+    #Boundary
+    points = [point_sw,   #se
+              point_nw,
+              point_dam_top,
+              point_ne, 
+              point_se, 
+              point_dam_bottom
+              ]
+    
+    segments = [[0,1], [1,2], [2,3],
+                        [3,4 ],[4,5], [5,0],  #The outer border
+                        [2,5]]         #dam Separator
+    
+    segment_tags = {'wall':[0,1,2,4,5],'edge':[3]} # '':[6]
+        
+    m.add_points_and_segments(points, segments, segment_tags)
+    
+    dam = m.add_region(-0.0000001,(ytop - ybottom)/2)
+    # this is the location of the region.
+    dam.setTag("dam")
+    
+    if is_coarse:
+        m.generate_mesh(maximum_triangle_area=0.05)
+    else:
+        m.generate_mesh(maximum_triangle_area=0.0001)
+
+    m.export_mesh_file(mesh_filename)
+    print "mesh created"
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    generate("aa.tsh", 0.75, is_course = True)
Index: /anuga_validation/uq_friction_2007/fromD_0.2_Slope0.05_x0.2-0.6_clean.csv
===================================================================
--- /anuga_validation/uq_friction_2007/fromD_0.2_Slope0.05_x0.2-0.6_clean.csv	(revision 4895)
+++ /anuga_validation/uq_friction_2007/fromD_0.2_Slope0.05_x0.2-0.6_clean.csv	(revision 4895)
@@ -0,0 +1,1500 @@
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+29.25,0.043,0.037,0.031,0.026,0.02
+29.27,0.042,0.037,0.032,0.026,0.02
+29.28,0.043,0.037,0.032,0.025,0.02
+29.31,0.043,0.037,0.032,0.026,0.021
+29.33,0.043,0.037,0.031,0.026,0.02
+29.34,0.043,0.037,0.032,0.026,0.02
+29.38,0.043,0.037,0.032,0.026,0.02
+29.39,0.043,0.037,0.032,0.026,0.02
+29.41,0.043,0.037,0.032,0.026,0.02
+29.44,0.042,0.037,0.032,0.026,0.02
+29.45,0.043,0.037,0.032,0.026,0.02
+29.47,0.043,0.037,0.032,0.026,0.02
+29.48,0.042,0.037,0.032,0.026,0.02
+29.52,0.042,0.037,0.032,0.026,0.02
+29.53,0.043,0.037,0.032,0.027,0.02
+29.55,0.043,0.037,0.032,0.026,0.02
+29.56,0.043,0.037,0.032,0.026,0.02
+29.59,0.043,0.037,0.031,0.026,0.02
+29.61,0.043,0.037,0.032,0.026,0.02
+29.63,0.042,0.037,0.032,0.027,0.02
+29.64,0.043,0.037,0.032,0.026,0.02
+29.67,0.042,0.037,0.032,0.026,0.02
+29.69,0.043,0.037,0.032,0.026,0.02
+29.7,0.043,0.037,0.032,0.026,0.02
+29.73,0.043,0.037,0.031,0.026,0.02
+29.75,0.042,0.037,0.032,0.026,0.02
+29.77,0.042,0.037,0.032,0.026,0.02
+29.78,0.042,0.037,0.032,0.026,0.02
+29.81,0.042,0.037,0.031,0.026,0.02
+29.83,0.042,0.037,0.031,0.026,0.02
+29.84,0.042,0.037,0.031,0.026,0.02
+29.88,0.043,0.037,0.031,0.026,0.02
+29.89,0.042,0.037,0.031,0.026,0.02
+29.91,0.043,0.037,0.031,0.026,0.02
+29.92,0.042,0.037,0.031,0.026,0.02
+29.95,0.042,0.037,0.031,0.026,0.02
+29.97,0.042,0.037,0.031,0.026,0.02
+29.98,0.042,0.037,0.031,0.026,0.02
+30.02,0.042,0.037,0.031,0.026,0.02
Index: /anuga_validation/uq_friction_2007/plot.py
===================================================================
--- /anuga_validation/uq_friction_2007/plot.py	(revision 4895)
+++ /anuga_validation/uq_friction_2007/plot.py	(revision 4895)
@@ -0,0 +1,90 @@
+
+def plot_compare_csv(location, file_sim, 
+                     file_exp, y_label,file_sim2=None,
+                     save_as=None,
+                     x_label='Time (s)',
+                     legend_sim='ANUGA simulation',
+                     legend_sim2=None,
+                     legend_exp='Measured flume result',
+                     is_interactive=False):
+    """ 
+    """
+    from pylab import ion, plot, xlabel, ylabel, close, legend, \
+         savefig
+    from anuga.shallow_water.data_manager import csv2dict
+
+
+
+    # Load in the csv files and convert info from strings to floats
+    simulation, _ = csv2dict(file_sim)
+    time_sim = [float(x) for x in simulation['time']]
+    quantity_sim = [float(x) for x in simulation[location]]
+
+
+    experiment, _ = csv2dict(file_exp)
+    time_exp = [float(x) for x in experiment['time']]
+    quantity_exp = [float(x) for x in experiment[location]]
+
+    if file_sim2 is not None:
+        simulation2, _ = csv2dict(file_sim2)
+        time_sim2 = [float(x) for x in simulation2['time']]
+        quantity_sim2 = [float(x) for x in simulation2[location]]
+
+        
+    if is_interactive:
+        ion()
+    
+    if file_sim2 is None:
+        plot(time_sim, quantity_sim, time_exp, quantity_exp)
+    else:
+        plot(time_sim, quantity_sim, time_sim2, quantity_sim2,
+             time_exp, quantity_exp, )
+        
+
+    # Add axis stuff and legend
+    xlabel(x_label)
+    ylabel(y_label)
+    if legend_sim2 is None:
+        legend((legend_sim, legend_exp))
+    else:
+        legend((legend_sim, legend_sim2, legend_exp))
+        
+    
+    if is_interactive:
+        # Wait for enter pressed
+        raw_input()
+
+    if save_as is not None:
+        savefig(save_as)
+    
+    #Need to close this plot
+    close()
+    
+
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    """ Plot the stage graph for the ANUGA validation papar
+    """
+
+    import project
+    import shutil
+    from os import sep, path
+
+    depth_file = "uq-friction-depth.eps"
+    
+    # create Depth plot
+    plot_compare_csv(location='0.4:0.2',  # testing location
+                     file_sim=project.depth_filename,
+                     file_sim2=project.depth_filename2,
+                     file_exp=project.experiment_depth_filename,
+                     legend_sim="ANUGA, Manning's friction 0.0",
+                     legend_sim2="ANUGA, Manning's friction 0.01",
+                     y_label='Water height (m)',
+                     save_as=depth_file)
+
+    #import sys; sys.exit() 
+    # Move the files to the dir where the paper is being put together
+    paper_dir = path.join('..','..','anuga_work','publications','anuga_2007')
+    dest = path.join(paper_dir, depth_file)
+    shutil.copyfile(depth_file,dest)
Index: /anuga_validation/uq_friction_2007/project.py
===================================================================
--- /anuga_validation/uq_friction_2007/project.py	(revision 4895)
+++ /anuga_validation/uq_friction_2007/project.py	(revision 4895)
@@ -0,0 +1,12 @@
+"""Common filenames and locations for topographic data, meshes and outputs.
+Also includes origin for slump scenario.
+"""
+
+mesh_filename = "mesh.tsh"
+depth_filename = "zz_test0.0_depth.csv"
+depth_filename2 = "zz_test0.01_depth.csv"
+experiment_depth_filename =  "fromD_0.2_Slope0.05_x0.2-0.6_clean.csv"
+
+velocity_x_filename =  "velocity_x.csv"
+velocity_y_filename =  "velocity_y.csv"
+experiment_vel_filename =  "velocity_x_experiment.csv"
Index: /anuga_validation/uq_friction_2007/run_dam.py
===================================================================
--- /anuga_validation/uq_friction_2007/run_dam.py	(revision 4895)
+++ /anuga_validation/uq_friction_2007/run_dam.py	(revision 4895)
@@ -0,0 +1,144 @@
+"""Script for running a dam break simulation of UQ's dam break tank,
+focusing on a friction comparison.
+
+The simulation will
+form part of the ANUGA validation paper.
+
+Ole Nielsen and Duncan Gray, GA - 2006 
+
+
+Issues
+If running this is hand-set-up parallel, the python files are overwritten.
+
+"""
+
+
+#----------------------------------------------------------------------------
+# Import necessary modules
+#----------------------------------------------------------------------------
+
+# Standard modules
+import time
+from time import localtime, strftime
+import sys
+from shutil import copy
+from os import path, sep
+from os.path import dirname  #, basename
+
+# Related major packages
+from anuga.shallow_water import Domain, Reflective_boundary, \
+                            Dirichlet_boundary, Time_boundary, File_boundary
+from anuga.abstract_2d_finite_volumes.region import Set_region 
+from anuga.fit_interpolate.interpolate import interpolate_sww2csv
+from anuga.shallow_water.data_manager import start_screen_catcher, \
+     copy_code_files
+
+
+# Scenario specific imports
+import project                 # Definition of file names and polygons
+import create_mesh
+
+
+def main(friction, is_trial_run=False):
+    if is_trial_run is True:
+        add = '_test'
+        yieldstep = 1
+        finaltime = 31
+    else:
+        add = ''
+        yieldstep = 0.01
+        finaltime = 31
+    basename = 'zz' + add + str(friction)
+    
+    mesh_filename = project.mesh_filename + add + '.msh'
+
+    #--------------------------------------------------------------------------
+    # Copy scripts to output directory and capture screen
+    # output to file
+    #--------------------------------------------------------------------------
+
+    
+    if is_trial_run is False:
+        start_screen_catcher('.', int(friction*100))
+
+    #-------------------------------------------------------------------------
+    # Create the triangular mesh
+    #-------------------------------------------------------------------------
+    
+    gate_position = 0.85
+    create_mesh.generate(mesh_filename,
+                         gate_position,
+                         is_coarse=is_trial_run) # this creates the mesh
+
+    #-------------------------------------------------------------------------
+    # Setup computational domain
+    #-------------------------------------------------------------------------
+    domain = Domain(mesh_filename, use_cache = False, verbose = True)
+   
+
+    print 'Number of triangles = ', len(domain)
+    print 'The extent is ', domain.get_extent()
+    print domain.statistics()
+
+    
+    domain.set_name(basename)
+    domain.set_datadir('.')
+    domain.set_quantities_to_be_stored(['stage', 'xmomentum', 'ymomentum'])
+    domain.set_minimum_storable_height(0.01)
+    #domain.set_store_vertices_uniquely(True)  # for writting to sww
+
+    #-------------------------------------------------------------------------
+    # Setup initial conditions
+    #-------------------------------------------------------------------------
+
+    slope = 0.05
+
+    def elevation_tilt(x, y):
+        return x*slope
+        
+    domain.set_quantity('stage', elevation_tilt)
+    domain.set_quantity('friction', friction) 
+    domain.set_quantity('elevation',elevation_tilt)
+
+    print 'Available boundary tags', domain.get_boundary_tags()
+    domain.set_region('dam','stage',0.20,
+                                 location = 'unique vertices') 
+
+    Br = Reflective_boundary(domain)
+    Bd = Dirichlet_boundary([0,0,0])  # to drain the water out.
+    domain.set_boundary( {'wall': Br, 'edge': Bd} )
+
+    #-------------------------------------------------------------------------
+    # Evolve system through time
+    #-------------------------------------------------------------------------
+    t0 = time.time()
+
+    for t in domain.evolve(yieldstep, finaltime):
+        domain.write_time()
+    
+        print 'That took %.2f seconds' %(time.time()-t0)
+        print 'finished'
+
+    points = [[gate_position - 0.65,0.2],
+              [gate_position - 0.55,0.2],
+              [gate_position - 0.45,0.2],
+              [gate_position - 0.35,0.2],
+              [gate_position - 0.25,0.2]
+              ]
+
+    #-------------------------------------------------------------------------
+    # Calculate gauge info
+    #-------------------------------------------------------------------------
+
+    interpolate_sww2csv(basename +".sww",
+                        points,
+                        basename + "_depth.csv",
+                        basename + "_velocity_x.csv",
+                        basename + "_velocity_y.csv")
+  
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    for friction in [ 0.0, 0.01]:
+        main(friction, is_trial_run = False)
+    
Index: /anuga_work/publications/anuga_2007/anuga_validation.tex
===================================================================
--- /anuga_work/publications/anuga_2007/anuga_validation.tex	(revision 4894)
+++ /anuga_work/publications/anuga_2007/anuga_validation.tex	(revision 4895)
@@ -486,4 +486,8 @@
 
 
+% Validation UQ flume
+% at X:\anuga_validation\uq_flume_2007
+% run run_dam.py to create sww file and .csv files
+% run plot.py to create graphs, and move them here
 \begin{figure}[htbp]
 \centerline{\includegraphics[width=4in]{uq-flume-depth.eps}}
@@ -507,4 +511,15 @@
 the reservoir gate is opened and the water flows into the other side
 of the flume.
+
+
+% Validation UQ friction
+% at X:\anuga_validation\uq_friction_2007
+% run run_dam.py to create sww file and .csv files
+% run plot.py to create graphs, and move them here
+\begin{figure}[htbp]
+\centerline{\includegraphics[width=4in]{uq-friction-depth.eps}}
+\caption{Comparison of wave tank and \ANUGA{} water height at .4 m
+  from the gate, simulated using a Mannings friction of 0.0 and 0.1.}\label{fig:uq-friction-depth}
+\end{figure}
 
 \section{Conclusions}
