slim3d benchmark: tilted thermocline under a constant wind stress

benchmarks/swe3d/stationnaryTiltedThermo/box.geo

+L = 10e3;
+l = 125;
+Point(1) = {-L, -l, 0,500};
+Point(2) = {L, -l, 0,500};
+Point(3) = {L, l, 0,500};
+Point(4) = {-L, l, 0,500};
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+Line Loop(1) = {3, 4, 1, 2};
+Plane Surface(1) = {1};
+
+
+Transfinite Line{2} = 2;
+Transfinite Line{4} = 2;
+
+
+Transfinite Line{1} = 81;
+Transfinite Line{3} = 81;
+
+Mesh.Algorithm=8;
+
+Recombine Surface{1};
+
+Physical Surface("sea")={1};
+Physical Line("coast") = {2,4};
+Physical Line("cut") = {3};
+Physical Line("paste") = {1};
+

benchmarks/swe3d/stationnaryTiltedThermo/box.msh

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benchmarks/swe3d/stationnaryTiltedThermo/computeError.py

+
+
+fslim = open('thermocline_slim.txt', 'r')
+ftheo = open('thermocline_theo.txt', 'r')
+
+emax = 0
+emean = 0
+n = 0
+ffact = 1/30.
+h0 = 50*ffact
+
+ls = fslim.readline()
+lt = ftheo.readline()
+while True:
+    if not ls: break
+    if not lt: break
+    (xs, ts) = (float(s) for s in ls.split(' '))
+    (xt, tt) = (float(s) for s in lt.split(' '))
+    if abs(xs-xt) > 1e-6: print("BUG here")
+    e = abs(ts-tt)/h0
+    emax = max(e, emax)
+    emean = emean + e
+    n = n+1
+    ls = fslim.readline()
+    lt = ftheo.readline()
+
+emean = emean / n
+print('emax : %g\n' % emax )
+print('emean: %g\n' % emean)
+

benchmarks/swe3d/stationnaryTiltedThermo/computeThermocline.py

+from dgpy import *
+import slim3d
+
+output_dir = 'output_3D/'
+lastExport = 200
+
+mesh3d_file = output_dir+'mesh2dxz.msh'
+domain = slim3d.Domain(mesh3d_file)
+slimSolver = domain._slimSolver
+groups3d = slimSolver.groups3d
+groups2d = slimSolver.groups2d
+extrusion = slimSolver.extrusion()
+
+TDof = dgDofContainer(groups3d, 1)
+zDof = dgDofContainer(groups3d, 1)
+thermoclineDof = dgDofContainer(groups2d, 1)
+exporter = dgIdxExporter(thermoclineDof, output_dir + '/thermocline');
+
+
+feval = dgFunctionEvaluator(groups2d, thermoclineDof.getFunction())
+val = fullMatrixDouble(1,1)
+nPoints = 50
+L = 550e3
+xfact = 1e-5
+ffact = -1/30.
+
+for iExport in range(lastExport+1):
+    print('Computing thermocline export %003d ' % iExport)
+    TDof.importIdx( (output_dir+"temperature/temperature-%06d.idx" % iExport) )
+    zDof.importIdx( (output_dir+"z/z-%06d.idx" % iExport) )
+    computeThermocline(extrusion, TDof, zDof, thermoclineDof, 24.8)
+    exporter.exportIdx(iExport, 0)
+    if iExport == 70:#lastExport:
+        f = open('thermocline_slim.txt', 'w')
+        for i in range(nPoints):
+            x = i * L / (nPoints-1)
+            feval.compute(x, 0, 0, val)
+            f.write('%g %g\n' % (x*xfact, val.get(0,0)*ffact) )
+        f.close()
+
+
+Msg.Exit(0)

benchmarks/swe3d/stationnaryTiltedThermo/run3d.py

+import slimPre
+import numpy as np
+
+data_dir = 'data3d/'
+slimPre.make_directory(data_dir)
+
+
+mesh_file = slimPre.fetch_ftp('slim_data/tanganyika/tanga1dx.msh')
+
+print('Extruding mesh')
+def shiftOperation(node, iPerBound) :
+  n = [node[0], node[1] - 1e4, node[2]]
+  return n
+cutTags = ["cut"]
+pasteTags = ["paste"]
+mapFilename = data_dir+"periodicMesh.txt"
+periodicity = (shiftOperation, cutTags, pasteTags, mapFilename)
+
+#mesh2d = slimPre.Mesh(mesh_file)
+#region_global = slimPre.Region(mesh2d)
+#xyz = region_global.coordinates
+#
+#bath_file_name = slimPre.fetch_ftp('slim_data/tanganyika/1d_bath.txt')
+#f = open(bath_file_name, 'r');
+#l = f.readline()
+#data = []
+#while l != '':
+#    (x1d, x, y, h) = [float(d) for d in l.split(',')]
+#    data.append([x1d, x, y, h])
+#    l = f.readline()
+#f.close()
+#data = np.array(data)
+#
+#bath = np.zeros((xyz.shape[0]))
+#for i in range(bath.shape[0]):
+#    x = xyz[i,0]
+#    ind = np.where(x < data[:,0])[0][0]
+#    if ind == 0:
+#        print('bug')
+#        exit(-1)
+#    xsi = (x-data[ind-1,0]) / (data[ind,0]-data[ind-1,0])
+#    bath[i] = (1-xsi) * data[ind-1,3] + xsi * data[ind,3]
+#
+#slimPre.write_file(data_dir+'bath_2d.nc', region=region_global, time=None, data=[('bath',bath)])
+#slimPre.netcdf_to_msh(mesh_file, data_dir+'bath_2d.nc','bath',data_dir+'bath')
+h = 700
+slimPre.write_file(data_dir+'bath_2d.nc', region=None, time=None, data=[('bath',h)])
+
+zLayers  = [0, 2, 5]
+zLayers += [10 * h for h in range(1, 11)]
+zLayers += [150, 200, 300, 500, 700, 950, 1200, 1400, 1500]
+mesh3d_file = data_dir+'tanga2dxz.msh'
+slimPre.extrude(mesh_file, (data_dir+'bath_2d.nc','bath'), z_layers=zLayers, mesh_file_name_out=mesh3d_file, factor_show=200, periodicity=periodicity)
+
+print('Loading 3D mesh')
+mesh = slimPre.Mesh(mesh3d_file)
+region_global = slimPre.Region(mesh)
+
+#print('Preprocessing Coriolis')
+#Tday = 0.99726968*24*60*60; # sidereal time of Earth revolution
+#OmegaEarth = 2*np.pi/Tday
+#latDeg = -6.2
+#phi = (np.pi/180)*latDeg # latitude in radians
+#corio = 2*OmegaEarth*np.sin(phi) # // [rad/s] Coriolis parameter
+#slimPre.write_file(data_dir+'coriolis.nc',None,None,[('coriolis',corio)])
+
+#print('Fixed viscosity')
+#import dgpy
+#shear = np.array([5, 5, 5, 1])/1e3
+#groups = mesh._groups
+#data = dgpy.fullMatrixDouble()
+#dof = dgpy.dgDofContainer(groups, 1)
+#dof_copy = dgpy.dgDofContainer(groups, 1)
+#dof.setAll(0)
+#for iFaceGroup in range(groups.getNbFaceGroups()):
+#    faceGroup = groups.getFaceGroup(iFaceGroup)
+#    if faceGroup.physicalTag() == 'vertical_bottom' or faceGroup.physicalTag() == 'bottom_sea':
+#        iGroup = groups.getElementGroupId(faceGroup.elementGroup(0))
+#        for iFace in range(faceGroup.size()):
+#            iElem = faceGroup.elementId(iFace, 0)
+#            dof.getElementProxy(iGroup, iElem, data)
+#            data.setAll(shear[0])
+#data0 = dgpy.fullMatrixDouble()
+#data1 = dgpy.fullMatrixDouble()
+#for i in range(len(shear)-1):
+#    dof_copy.copy(dof)
+#    for iFaceGroup in range(groups.getNbFaceGroups()):
+#        faceGroup = groups.getFaceGroup(iFaceGroup)
+#        if faceGroup.nConnection() == 2:
+#            iGroup0 = groups.getElementGroupId(faceGroup.elementGroup(0))
+#            iGroup1 = groups.getElementGroupId(faceGroup.elementGroup(1))
+#            for iFace in range(faceGroup.size()):
+#                iElem0 = faceGroup.elementId(iFace, 0)
+#                iElem1 = faceGroup.elementId(iFace, 1)
+#                dof_copy.getElementProxy(iGroup0, iElem0, data0)
+#                dof.getElementProxy(iGroup1, iElem1, data1)
+#                if data0.get(0,0) > 1e-10 and data1.get(0,0) < 1e-10:
+#                    data1.setAll(shear[i+1])