Index: /inundation/validation/Incomplete/LWRU1/benchmark_1.txt
===================================================================
--- /inundation/validation/Incomplete/LWRU1/benchmark_1.txt	(revision 1774)
+++ /inundation/validation/Incomplete/LWRU1/benchmark_1.txt	(revision 1774)
@@ -0,0 +1,1015 @@
+Benchmark # 1 -- runup on a uniformly sloping beach: 1-D problem.
+
+Compute the snap shots of water-surface and velocity profiles at t = 160 sec., 175 
+sec, and 220 sec.  
+Also compute the temporal variations of the shoreline location (xs) and shoreline 
+velocity (us) from 
+t = 100 sec. to 280 sec.
+
+Beach slope = 1/10
+
+Initial water surface displacement, and velocity = 0, everywhere at t = 0.
+
+x (m) 	eta (m)
+0	0.001386879
+50	0.001418557
+100	0.001448675
+150	0.001476851
+200	0.001502653
+250	0.001525595
+300	0.001545127
+350	0.001560637
+400	0.001571436
+450	0.001576752
+500	0.001575726
+550	0.0015674
+600	0.001550705
+650	0.001524456
+700	0.001487337
+750	0.001437888
+800	0.001374497
+850	0.001295378
+900	0.001198562
+950	0.00108188
+1000	0.000942942
+1050	0.000779122
+1100	0.000587533
+1150	0.000365013
+1200	0.000108095
+1250	-0.000187012
+1300	-0.000524455
+1350	-0.000908755
+1400	-0.001344846
+1450	-0.001838098
+1500	-0.002394354
+1550	-0.00301996
+1600	-0.003721805
+1650	-0.004507353
+1700	-0.005384687
+1750	-0.006362547
+1800	-0.007450373
+1850	-0.008658349
+1900	-0.009997448
+1950	-0.011479481
+2000	-0.013117144
+2050	-0.014924068
+2100	-0.016914873
+2150	-0.019105216
+2200	-0.021511848
+2250	-0.024152665
+2300	-0.027046767
+2350	-0.030214509
+2400	-0.033677557
+2450	-0.037458945
+2500	-0.041583128
+2550	-0.046076034
+2600	-0.050965122
+2650	-0.056279425
+2700	-0.062049605
+2750	-0.068307999
+2800	-0.075088659
+2850	-0.082427396
+2900	-0.090361815
+2950	-0.098931345
+3000	-0.10817727
+3050	-0.118142745
+3100	-0.128872819
+3150	-0.140414434
+3200	-0.152816431
+3250	-0.166129544
+3300	-0.180406381
+3350	-0.195701401
+3400	-0.212070878
+3450	-0.229572857
+3500	-0.248267096
+3550	-0.268215
+3600	-0.289479539
+3650	-0.312125157
+3700	-0.336217664
+3750	-0.361824121
+3800	-0.389012704
+3850	-0.417852558
+3900	-0.44841364
+3950	-0.480766537
+4000	-0.514982285
+4050	-0.55113216
+4100	-0.589287466
+4150	-0.629519299
+4200	-0.671898307
+4250	-0.716494437
+4300	-0.763376645
+4350	-0.812612645
+4400	-0.8642686
+4450	-0.918408824
+4500	-0.975095469
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+4600	-1.096343923
+4650	-1.161016343
+4700	-1.228455744
+4750	-1.298708591
+4800	-1.371817204
+4850	-1.447819424
+4900	-1.526748269
+4950	-1.608631608
+5000	-1.693491827
+5050	-1.781345512
+5100	-1.872203133
+5150	-1.966068741
+5200	-2.062939676
+5250	-2.162806291
+5300	-2.265651683
+5350	-2.371451433
+5400	-2.480173427
+5450	-2.59177757
+5500	-2.70621564
+5550	-2.823431106
+5600	-2.94335898
+5650	-3.06592569
+5700	-3.191048978
+5750	-3.318637827
+5800	-3.448592406
+5850	-3.58080405
+5900	-3.715155257
+5950	-3.851519724
+6000	-3.989762401
+6050	-4.129739578
+6100	-4.271298998
+6150	-4.414279999
+6200	-4.558513686
+6250	-4.703823128
+6300	-4.850023589
+6350	-4.996922778
+6400	-5.144321137
+6450	-5.292012151
+6500	-5.439782687
+6550	-5.58741336
+6600	-5.734678926
+6650	-5.881348704
+6700	-6.02718702
+6750	-6.171953678
+6800	-6.315404461
+6850	-6.457291647
+6900	-6.597364561
+6950	-6.735370141
+7000	-6.871053531
+7050	-7.004158697
+7100	-7.13442906
+7150	-7.261608157
+7200	-7.385440311
+7250	-7.505671328
+7300	-7.622049208
+7350	-7.73432487
+7400	-7.842252895
+7450	-7.945592275
+7500	-8.044107177
+7550	-8.137567719
+7600	-8.225750741
+7650	-8.308440589
+7700	-8.385429907
+7750	-8.456520381
+7800	-8.521523565
+7850	-8.580261612
+7900	-8.632568033
+7950	-8.678288437
+8000	-8.717281245
+8050	-8.749418381
+8100	-8.774585933
+8150	-8.792684782
+8200	-8.803631188
+8250	-8.807357334
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+9100	-7.784065634
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+9200	-7.542729099
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+9750	-5.921759116
+9800	-5.758174032
+9850	-5.593227037
+9900	-5.427222643
+9950	-5.26046037
+10000	-5.093233695
+10050	-4.925829065
+10100	-4.758524964
+10150	-4.591591061
+10200	-4.42528743
+10250	-4.259863844
+10300	-4.095559149
+10350	-3.932600726
+10400	-3.77120402
+10450	-3.611572165
+10500	-3.453895679
+10550	-3.298352239
+10600	-3.145106536
+10650	-2.994310197
+10700	-2.846101782
+10750	-2.700606845
+10800	-2.557938053
+10850	-2.418195373
+10900	-2.281466301
+10950	-2.147826147
+11000	-2.01733836
+11050	-1.890054895
+11100	-1.76601661
+11150	-1.645253691
+11200	-1.527786148
+11250	-1.413624219
+11300	-1.302768919
+11350	-1.195212528
+11400	-1.090939108
+11450	-0.989925023
+11500	-0.892139465
+11550	-0.797544971
+11600	-0.706097946
+11650	-0.617749174
+11700	-0.532444323
+11750	-0.450124438
+11800	-0.37072642
+11850	-0.2941835
+11900	-0.220425684
+11950	-0.149380187
+12000	-0.080971874
+12050	-0.015123622
+12100	0.048243274
+12150	0.109208742
+12200	0.167853593
+12250	0.224259202
+12300	0.278507202
+12350	0.330679203
+12400	0.38085653
+12450	0.429119979
+12500	0.475549594
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+12650	0.604620415
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+12800	0.719956554
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+13150	0.946252721
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+13300	1.028905882
+13350	1.054944815
+13400	1.08030739
+13450	1.105038199
+13500	1.129179719
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+13600	1.175854426
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+13700	1.220630429
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+13850	1.284811872
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+14350	1.481234451
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+15850	2.013308145
+15900	2.030382385
+15950	2.047407193
+16000	2.064380161
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+16100	2.098160374
+16150	2.114962276
+16200	2.131701664
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+16350	2.181515598
+16400	2.197975461
+16450	2.214357776
+16500	2.230659377
+16550	2.246877059
+16600	2.26300758
+16650	2.27904767
+16700	2.294994031
+16750	2.310843342
+16800	2.326592264
+16850	2.342237442
+16900	2.35777551
+16950	2.373203091
+17000	2.388516803
+17050	2.403713262
+17100	2.41878908
+17150	2.433740874
+17200	2.448565264
+17250	2.463258875
+17300	2.477818341
+17350	2.492240309
+17400	2.506521436
+17450	2.520658395
+17500	2.534647874
+17550	2.54848658
+17600	2.562171241
+17650	2.575698605
+17700	2.589065444
+17750	2.602268555
+17800	2.615304762
+17850	2.628170916
+17900	2.640863898
+17950	2.65338062
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+21000	2.990363869
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+21100	2.985316269
+21150	2.982398627
+21200	2.979219488
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+21300	2.972080318
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+	
Index: /inundation/validation/Incomplete/LWRU1/icplot.py
===================================================================
--- /inundation/validation/Incomplete/LWRU1/icplot.py	(revision 1774)
+++ /inundation/validation/Incomplete/LWRU1/icplot.py	(revision 1774)
@@ -0,0 +1,35 @@
+
+filename = 'lwru1_IC.txt'
+
+
+#x = []
+#w = []
+#fid = open(filename)
+#for line in fid.readlines():
+#    fields = line.split()
+#    assert len(fields) == 2, '%s' %fields
+#    x.append( float(fields[0]) )
+#    w.append( float(fields[1]) )            
+#
+#print 'X', x, len(x)
+#print 'W', w, len(w)
+
+from pylab import plot, load, ion, ioff, draw, show, sin, hold
+
+X = load(filename)
+ion()
+plot(X[:,0], X[:,1])
+#draw()
+
+hold(False)
+for i in range(100000):
+    print i*i
+    plot(X[:,0], X[:,1] + sin(i/10.0))    
+
+
+
+show()
+print 'end'    
+
+
+
Index: /inundation/validation/Incomplete/LWRU1/lwru1.py
===================================================================
--- /inundation/validation/Incomplete/LWRU1/lwru1.py	(revision 1774)
+++ /inundation/validation/Incomplete/LWRU1/lwru1.py	(revision 1774)
@@ -0,0 +1,220 @@
+"""Example of shallow water wave equation.
+
+This script sets up a 2D version of the 1D LWRU1 benchmark with initial condition stated in the file benchmark_1.txt.
+
+See also
+
+http://www.cee.cornell.edu/longwave/index.cfm?page=benchmark&problem=1
+
+
+"""
+
+######################
+# Module imports
+
+from pyvolution.shallow_water import Domain, Reflective_boundary,\
+     Dirichlet_boundary,Transmissive_boundary, Constant_height, Constant_stage
+
+from pyvolution.mesh_factory import rectangular
+from Numeric import array, zeros, Float, allclose
+
+
+#######################
+# Domain
+#
+
+
+print 'Creating domain'
+#Create basic mesh
+#
+#The initial condition extends 50km off shore
+#and 5,000m is allowed on shore for wetting
+#(only about 200m is expected, though)
+
+points, vertices, boundary = rectangular(400, 40,
+                                         len1=55000, len2=5000,
+                                         origin = (-5000, 0.0))
+
+#points, vertices, boundary = rectangular(100, 10,
+#                                         len1=55000, len2=5000,
+#                                         origin = (-5000, 0.0))
+
+
+#Create shallow water domain
+domain = Domain(points, vertices, boundary)
+
+domain.check_integrity()
+domain.default_order = 2
+
+#Output params
+domain.smooth = True
+domain.reduction = min  #Looks a lot better on top of steep slopes
+print "Number of triangles = ", len(domain)
+
+domain.visualise = False
+domain.store = True    #Store for visualisation purposes
+domain.format = 'sww'   #Native netcdf visualisation format
+
+import sys, os
+base = os.path.basename(sys.argv[0])
+domain.filename, _ = os.path.splitext(base)
+
+
+#Set initial values
+def slope(x, y):
+    return -x/10
+
+
+class IC_x:
+    """
+    Read 1D initial condition and provide values at any x, y
+
+    File is assumed to list x values in the first column and
+    stage in the second.
+    """
+
+    def __init__(self, filename):
+
+        self.x = []
+        self.w = []
+        fid = open(filename)
+        for line in fid.readlines():
+            fields = line.split()
+            assert len(fields) == 2, '%s' %fields
+            self.x.append( float(fields[0]) )
+            self.w.append( float(fields[1]) )            
+
+        #print 'X', self.x, len(self.x)
+        #print 'W', self.w, len(self.w)
+        #from pylab import plot, show
+        #plot(self.x, self.w)
+        #show()
+        #import sys; sys.exit() 
+
+    def __call__(self, x, y):
+
+        w = zeros( len(x), Float )
+        for i in range(len(x)):
+            xi = x[i]
+
+            
+            #Find slot
+
+            if xi < self.x[0]: w[i] = self.w[0]
+            elif xi > self.x[-1]: w[i] = self.w[-1]
+            else:
+                index = 0
+                while xi > self.x[index]: index += 1
+                while xi < self.x[index]: index -= 1
+
+                #print xi, index, self.x[index], self.w[index]                    
+
+                if xi == self.x[index]:
+                #if allclose(xi, self.x[index]):
+                    #Protect against case where x is the last value
+                    # - also works in general when x == self.x[i]
+                    ratio = 0
+                else:
+                    #x is now between index and index+1
+                    ratio = (xi - self.x[index])/\
+                            (self.x[index+1] - self.x[index])
+
+                #print xi, index, self.x[index], ratio
+
+                #Compute interpolated value
+                if ratio > 0:
+                    w[i] = self.w[index] +\
+                           ratio*(self.w[index+1] - self.w[index])
+                else:
+                    w[i] = self.w[index]
+
+        #print x, w            
+        return w    
+
+
+
+print 'Field values'
+domain.set_quantity('elevation', slope)
+domain.set_quantity('friction', 0.0)
+domain.set_quantity('stage', IC_x('lwru1_IC.txt'))
+
+#import sys; sys.exit()
+
+#print domain.quantities['stage'].centroid_values
+
+######################
+# Boundary conditions
+#
+print 'Boundaries'
+Br = Reflective_boundary(domain)
+Bt = Transmissive_boundary(domain)
+
+#Constant inflow
+Bd = Dirichlet_boundary([0.0, 0.0, 0.0])
+
+#Set boundary conditions
+domain.set_boundary({'left': Br, 'right': Bt, 'bottom': Bt, 'top': Bt})
+
+
+#Evolve
+import time
+t0 = time.time()
+
+
+
+
+pt = []
+xes = []
+y = 2500 
+x0 = -100
+step = 50
+for i in range(1000):
+    x = x0+i*step
+    xes.append(x)
+    pt.append( [x,y] )
+
+from pylab import *
+from pyvolution.least_squares import Interpolation
+
+ 
+V = domain.get_vertex_coordinates(obj=True) #Why?
+T = domain.get_triangles(obj=True)
+
+
+I = Interpolation(V,
+                  T,
+                  point_coordinates = pt,
+                  verbose = True)
+
+
+f = domain.quantities['elevation'].vertex_values.flat
+z = I.interpolate( f )
+
+print 'xxxxx'
+
+ion()
+hold(False)
+f = domain.quantities['stage'].vertex_values.flat
+y = I.interpolate( f )
+plot(xes, y, '-b', xes, z, '-k')
+set( gca(), Ylim=(-10,10) )
+
+raw_input('go')
+for t in domain.evolve(yieldstep = 1, finaltime = 300.0):
+
+    f = domain.quantities['stage'].vertex_values.flat
+    y = I.interpolate( f )
+    ioff()
+    plot(xes, y, '-b', xes, z, '-k')
+    ion()
+    set( gca(), Ylim=(-10,10) )
+    
+    
+    #print y[:], y.shape
+
+
+    domain.write_time()
+
+
+print 'That took %.2f seconds' %(time.time()-t0)
+show()
Index: /inundation/validation/Incomplete/LWRU1/lwru1_IC.txt
===================================================================
--- /inundation/validation/Incomplete/LWRU1/lwru1_IC.txt	(revision 1774)
+++ /inundation/validation/Incomplete/LWRU1/lwru1_IC.txt	(revision 1774)
@@ -0,0 +1,1001 @@
+0	0.001386879
+50	0.001418557
+100	0.001448675
+150	0.001476851
+200	0.001502653
+250	0.001525595
+300	0.001545127
+350	0.001560637
+400	0.001571436
+450	0.001576752
+500	0.001575726
+550	0.0015674
+600	0.001550705
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+700	0.001487337
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