Ran validations and added report to doc directory

.gitignore

@@ -24,14 +24,57 @@
 *.dem
 *.asc
 *.qgs
+*.aux
+*.bbl
+*.blg
+*.out
+*.toc
 tags
+
+# validation temp files #
+#########################
 parameters.tex
 ch5.png
 ch7.png
 ch9.png
 Boundary.png
 Benchmark_2_Bathymetry.xya
 Benchmark_2_input.tms
+report.pdf
+LEFT_REACH.png
+MIDDLE_REACH.png
+RIGHT_REACH.png
+riverwall_points
+vel_t1_centroid.png
+vel_t1_vertex.png
+vel_t2_centroid.png
+vel_t2_vertex.png
+xvelocity_at_y05.png
+rmom_plot.png
+rvel_plot.png
+stage_plot.png
+saved_parameters.tex
+CENTRAL_CHANNEL.png
+xmom*.png
+xvel*.png
+ymom*.png
+Xmom*.png
+Xvel*.png
+x_velocity.png
+y_velocity.png
+depth_y.png
+depth_x.png
+Shoreline_position.png
+Shoreline_velocity.png
+figure_*.png
+cross_section_*.png
+stage*.png
+Stage*.png
+force.png
+Fluxes.png
+fig*.png
+perturbation_at_origin.png
+wave_atten.png
 
 # Compiled source #
 ###################

validation_tests/analytical_exact/dam_break_wet/numerical_dam_break_wet.py

@@ -88,17 +88,11 @@ def height(x,y):
 # Associate boundary tags with boundary objects
 domain.set_boundary({'left': Bt, 'right': Bt, 'top': Br, 'bottom': Br})
 
-#------------------------------------------------------------------------------
+#-------------------------------------------------------------------------
 # Produce a documentation of parameters
-#------------------------------------------------------------------------------
-if myid == 0:
-    parameter_file=open('parameters.tex', 'w')
-    parameter_file.write('\\begin{verbatim}\n')
-    from pprint import pprint
-    pprint(domain.get_algorithm_parameters(),parameter_file,indent=4)
-    parameter_file.write('\\end{verbatim}\n')
-    parameter_file.close()
-
+#-------------------------------------------------------------------------
+from anuga.validation_utilities import save_parameters_tex
+save_parameters_tex(domain)
 
 #===================================================================================
 # Evolve system through time

validation_tests/behaviour_only/bridge_hecras/channel_floodplain1.py

@@ -233,6 +233,6 @@ def outflow_stage_boundary(t):
     if(myid==0 & verbose):
         print domain.timestepping_statistics()
 
-doamin.sww_merge(delete_old=True)
+domain.sww_merge(delete_old=True)
 
 finalize()

validation_tests/experimental_data/dam_break_yeh_petroff/numerical_Yeh_Petroff.py

@@ -16,52 +16,27 @@
 #from balanced_dev import *
 from anuga.geometry.polygon import inside_polygon, is_inside_triangle
 
+from anuga import distribute, myid, numprocs, finalize, barrier
+
+#================================================================================
+# Setup parameters and globally used functions
+#================================================================================
 
 args = anuga.get_args()
 alg = args.alg
 verbose = args.verbose
 
-#-------------------------------------------------------------------------------
-# Copy scripts to time stamped output directory and capture screen
-# output to file
-#-------------------------------------------------------------------------------
-time = strftime('%Y%m%d_%H%M%S',localtime())
-
-#output_dir = 'dam_break_'+time
-output_dir = '.'
-output_file = 'dam_break'
-
-#anuga.copy_code_files(output_dir,__file__)
-#start_screen_catcher(output_dir+'_')
 
+time = strftime('%Y%m%d_%H%M%S',localtime())
 
-#------------------------------------------------------------------------------
-# Setup domain
-#------------------------------------------------------------------------------
 dx = 0.01
 dy = dx
 L = 1.6
 W = 0.61
 
-# structured mesh
-points, vertices, boundary = anuga.rectangular_cross(int(L/dx), int(W/dy), L, W, (0.0, 0.0))
-
-#domain = anuga.Domain(points, vertices, boundary) 
-domain = Domain(points, vertices, boundary) 
-
-domain.set_name(output_file)                
-domain.set_datadir(output_dir) 
-
-#------------------------------------------------------------------------------
-# Setup Algorithm, either using command line arguments
-# or override manually yourself
-#------------------------------------------------------------------------------
-domain.set_flow_algorithm(alg)
-
-
-#------------------------------------------------------------------------------
+#-------------------------------
 # Setup initial conditions
-#------------------------------------------------------------------------------
+#-------------------------------
 def stage(x,y):
     h = zeros(len(x), float)
     for i in range(len(x)):
@@ -85,9 +60,43 @@ def elevation(x,y):
             if 0.25 <= y[i] <= 0.25+0.12:
                 z[i] = 0.75
     return z
-domain.set_quantity('stage', stage)
-domain.set_quantity('elevation',elevation)
-domain.set_quantity('friction', 0.03)
+
+
+
+#================================================================================
+# create sequential domain
+#================================================================================
+if myid == 0:
+    # structured mesh
+    points, vertices, boundary = anuga.rectangular_cross(int(L/dx), int(W/dy), L, W, (0.0, 0.0))
+
+    #domain = anuga.Domain(points, vertices, boundary) 
+    domain = Domain(points, vertices, boundary) 
+
+    domain.set_name(output_file)                
+    domain.set_datadir(output_dir) 
+
+    #------------------------------------------------------------------------------
+    # Setup Algorithm, either using command line arguments
+    # or override manually yourself
+    #------------------------------------------------------------------------------
+    domain.set_flow_algorithm(alg)
+
+
+    domain.set_quantity('stage', stage)
+    domain.set_quantity('elevation',elevation)
+    domain.set_quantity('friction', 0.03)
+
+else:
+
+    domain = None
+
+
+#===================================================================================
+# create parallel domain
+#===================================================================================
+domain = distribute(domain)
+
 
 #-----------------------------------------------------------------------------
 # Setup boundary conditions
@@ -101,78 +110,22 @@ def elevation(x,y):
 domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
 
 
-#===============================================================================
-##from anuga.visualiser import RealtimeVisualiser
-##vis = RealtimeVisualiser(domain)
-##vis.render_quantity_height("stage", zScale =h0*500, dynamic=True)
-##vis.colour_height_quantity('stage', (0.0, 0.5, 1.0))
-##vis.start()
-#===============================================================================
-
-
-#---------------------------------------------
-# Find triangle that contains the point Point
-# and print to file
-#---------------------------------------------
-##PointL = []
-##print "0.12/dx=",int(round(0.12/dx))
-##STOP
-##PointL=[(0.868, 0.255),
-##          (0.868, 0.265),
-##          (0.868, 0.275),
-##          (0.868, 0.285),
-##          (0.868, 0.295),
-##          (0.868, 0.305),
-##          (0.868, 0.315),
-##          (0.868, 0.325),
-##          (0.868, 0.335),
-##          (0.868, 0.345),
-##          (0.868, 0.355),
-##          (0.868, 0.365)]
-###PointR = []
-##PointR=[(1.032, 0.255),
-##          (1.032, 0.265),
-##          (1.032, 0.275),
-##          (1.032, 0.285),
-##          (1.032, 0.295),
-##          (1.032, 0.305),
-##          (1.032, 0.315),
-##          (1.032, 0.325),
-##          (1.032, 0.335),
-##          (1.032, 0.345),
-##          (1.032, 0.355),
-##          (1.032, 0.365)]
-##for i in range(len(PointR)):
-##    Point = PointR[i]
-##    for n in range(len(domain.triangles)):
-##        tri = domain.get_vertex_coordinates(n)
-##        if is_inside_triangle(Point,tri):
-##            #print 'Point is within triangle with vertices '+'%s'%tri
-##            n_point = n
-##            break
-##    print 'n_point = ',n_point
-
-
-#------------------------------------------------------------------------------
+#-------------------------------------------------------------------------
 # Produce a documentation of parameters
-#------------------------------------------------------------------------------
-parameter_file=open('parameters.tex', 'w')
-parameter_file.write('\\begin{verbatim}\n')
-from pprint import pprint
-pprint(domain.get_algorithm_parameters(),parameter_file,indent=4)
-parameter_file.write('\\end{verbatim}\n')
-parameter_file.close()
+#-------------------------------------------------------------------------
+from anuga.validation_utilities import save_parameters_tex
+save_parameters_tex(domain)
+
 
 #------------------------------------------------------------------------------
 # Evolve system through time
 #------------------------------------------------------------------------------
 for t in domain.evolve(yieldstep = 0.05, finaltime = 3.0):
-    #print domain.timestepping_statistics(track_speeds=True)
-    print domain.timestepping_statistics()
-    #vis.update()
+    if myid == 0 and verbose:
+        print domain.timestepping_statistics()
 
 
-#test against know data
-    
-#vis.evolveFinished()
+domain.sww_merge(delete_old=True)
+
+finalize()
 

validation_tests/reports/all_tests_report.tex → validation_tests/reports/validations_report.tex

@@ -7,6 +7,8 @@
 \usepackage{hyperref}
 \usepackage{url}
 \usepackage{amsmath}
+\usepackage{titlesec}
+\newcommand{\sectionbreak}{\clearpage}
 \DeclareUrlCommand\UScore{\urlstyle{rm}}
 
 
@@ -46,36 +48,58 @@ \chapter{Introduction}
 
 The results in this report were produced by \anuga{} version \majorR{} from svn
 repository revision \minorR{} at time \timeR.
-The flow algorithm was \alg{}, unless otherwise stated explicitly. Based   on this version, 26 tests are available in the subversion. To get an automated report, we can run either an individual run of the available tests or the complete (whole) test.
+The flow algorithm was \alg{}, unless otherwise stated explicitly. Based on this version, 
+26 tests are available in the subversion. To get an automated report, 
+we can run either an individual run of the available tests or the complete (whole) test.
 
 To do an individual test, we can run the python module \\
 \verb produce_results.py \\
-available in the corresponding test directory. The module will do the numerical simulation of the given problem, plot the simulation results in png files, and type-set the corresponding individual automated report. The individual automated report is in pdf file and saved in the same directory.
+available in the corresponding test directory. The module will do the 
+numerical simulation of the given problem, plot the simulation 
+results in png files, and type-set the corresponding 
+individual automated report. The individual automated report is in 
+pdf file and saved in the same directory.
 
 To do the complete test, we can just run the python module \\
 \verb all_tests_produce_results.py \\
 available in the directory \\
 \verb validation_tests/reports \\
-Similar to the module for an individual test, this python module will do the numerical simulations of all the given problems, plot results in png files and save them in its corresponding directory, and finally type-set the complete report. The complete automated report is saved in this directory.
-
-The simulation results can be analysed qualitatively and quantitatively. Qualitative analysis can be done by investigating the plots of the results whether they are physical or not, and whether the behaviour is the same as we expected. Quantitative analysis can be conducted by checking the numerical error. We have provided python module with the name begun by the word ``validate'' in each of individual tests. We can also run validate$\_$all.py to measure the numerical errors from the directory \verb run_auto_validation_tests . This validate$\_$all.py will run a subset of the available tests having sensible ``correct'' results to test against.
-
-The main parameters in the validations are the Courant--Friedrichs-Lewy (CFL) number and the flow algorithm. They are spelled ``cfl'' and ``alg'' respectively in the python module \\
+Similar to the module for an individual test, this python module 
+will do the numerical simulations of all the given problems, 
+plot results in png files and save them in its corresponding directory, 
+and finally type-set the complete report. The complete automated report is saved in this directory.
+
+The simulation results can be analysed qualitatively and quantitatively. 
+Qualitative analysis can be done by investigating the plots of 
+the results whether they are physical or not, and whether the 
+behaviour is the same as we expected. Quantitative analysis can 
+be conducted by checking the numerical error. 
+
+We have also provided a python script \verb run_auto_validation_tests.py in 
+the \verb validation_tests  directory which will run a subset of the available tests 
+having sensible ``correct'' results to test against.
+
+The main parameters in the validations are the Courant--Friedrichs-Lewy (CFL) 
+number and the flow algorithm. They are spelled 
+\verb cfl  and \verb alg  respectively in the python module \\
 \verb parameters \\
 which is available in the \\
 \verb anuga.validation_tests \\
-module. In the default setting, we set the CFL to be $1.0$ and the flow algorithm to be DE0 (second order in space and first order in time). The complete available flow algorithms are as follow:
-'1$\_$0', '1$\_$5', '1$\_$75', '2$\_$0', '2$\_$0$\_$limited', '2$\_$5', 'tsunami', 'yusuke', 'DE0', 'DE1', 'DE2'.
-%\begin{enumerate}
-%\item '1$\_$0', 
-%\item '1$\_$5', 
-%\item '1$\_$75', 
-%\item '2$\_$0', 
-%\item '2$\_$0$\_$limited', 
-%\item '2$\_$5', 
-%\item 'tsunami', 
-%\item 'yusuke'.
-%\end{enumerate}
+module. In the default setting, we set the CFL to be $1.0$ and 
+the flow algorithm to be \verb DE0  (second order in space and first order in time). 
+The complete available flow algorithms are as follow:
+\verb 1_0 ,
+\verb 1_5 , 
+\verb 1_75 , 
+\verb 2_0 , 
+\verb 2_0_limited , 
+\verb 2_5 ,
+\verb tsunami , 
+\verb yusuke , 
+\verb DE0 , 
+\verb DE1 , 
+\verb DE2 .
+
 They can be found in \\
 \verb \anuga_core\source\anuga\shallow_water\shallow_water_domain.py .
 
@@ -161,16 +185,25 @@ \section{Algorithm Parameters}
 \verb|anuga.validation_utilities.parameters|. 
 
 In particular the
-values of \verb|alg| (flow algorithm) and \verb|cfl| (CFL Condition)
-are passed as command options when calling \verb|produce_results.py| in the
+values of \verb alg  (flow algorithm) and \verb cfl  (CFL Condition)
+are passed as command options when calling \verb produce_results.py  in the
 test directories.
 
+Within \anuga{} script you can obtain command line parameters via
+\begin{verbatim}
+args = anuga.get_args()
+alg = args.alg
+verbose = args.verbose
+\end{verbatim}
+to obtain the values of \verb alg (flow algorithm) and \verb verbose (flag)
+
 You can pass though the standard parameters as follows
 \begin{verbatim}
 from anuga.validation_utilities.parameters import alg
 from anuga.validation_utilities.parameters import cfl
 \end{verbatim}
 
+\pagebreak
 \section{Generic form of \texttt{produce\_results.py}}
 
 The \texttt{produce\_results.py} files in the test directories should have the