slim3d: adaption on a rofi

benchmarks/swe3d/rofiAdapt/box.geo

+L = 30e3;
+l = 1e3/5;
+Point(1) = {-L, -l, 0};
+Point(2) = {L, -l, 0};
+Point(3) = {L, l, 0};
+Point(4) = {-L, l, 0};
+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} = 25*5;
+Transfinite Line{3} = 25*5;
+
+Mesh.Algorithm=8;
+
+Recombine Surface{1};
+
+Physical Surface("sea")={1};
+Physical Line("open") = {2};
+Physical Line("river") = {4};
+Physical Line("cut") = {3};
+Physical Line("paste") = {1};
+

benchmarks/swe3d/rofiAdapt/opt.opt

+General.ExecutableFileName = "/home/delandmeter/sources/gmsh/projects/dg/build/gmsh/gmsh";
+General.FileName = "output_sigma/mesh3d_show.msh";
+General.RecentFile0 = "output_sigma/mesh3d_show.msh";
+General.RecentFile1 = "data/mesh3d_show.msh";
+General.RecentFile2 = "box.geo";
+General.RecentFile3 = "box.msh";
+General.RecentFile4 = "boxShow.msh";
+General.RecentFile5 = "boxSigma.msh";
+General.RecentFile6 = "sigmaShow.msh";
+General.RecentFile7 = "sigmaShow.msh";
+General.RecentFile8 = "sigmaShow.msh";
+General.RecentFile9 = "sigmaShow.msh";
+General.BoundingBoxSize = 60828.94048066266;
+General.ClipPositionX = 1555;
+General.ClipPositionY = 676;
+General.ColorScheme = 0;
+General.ContextPositionX = 1485;
+General.FieldPositionX = 84;
+General.FieldPositionY = 187;
+General.FieldHeight = 601;
+General.FieldWidth = 903;
+General.GraphicsHeight = 531;
+General.GraphicsPositionX = 2085;
+General.GraphicsPositionY = 124;
+General.GraphicsWidth = 1674;
+General.MaxX = 30000;
+General.MaxY = 200;
+General.MenuWidth = 167;
+General.MenuPositionX = 665;
+General.MenuPositionY = 624;
+General.MessageHeight = 140;
+General.MinX = -30000;
+General.MinY = -200;
+General.MinZ = -10000;
+General.OptionsPositionX = 2400;
+General.OptionsPositionY = 591;
+General.PluginPositionX = 4475;
+General.PluginPositionY = 1598;
+General.PluginHeight = 641;
+General.PluginWidth = 1284;
+General.RotationX = 270;
+General.ScaleX = 1.351610329695492;
+General.ScaleY = 1.351610329695492;
+General.ScaleZ = 1.351610329695492;
+General.StatisticsPositionX = 347;
+General.StatisticsPositionY = 561;
+General.TrackballQuaternion0 = 0.7071067811865475;
+General.TrackballQuaternion3 = 0.7071067811865476;
+General.TranslationX = -134.7443156599955;
+General.TranslationY = 1433.670218212546;
+General.VisibilityPositionX = 1235;
+General.VisibilityPositionY = 410;
+Mesh.ChacoHypercubeDim = 0;
+Mesh.ChacoMeshDim1 = 1;
+Mesh.NbHexahedra = 1240;
+Mesh.NbNodes = 2750;
+Mesh.NbQuadrangles = 2748;
+Mesh.RemeshParametrization = 0;
+Mesh.SurfaceEdges = 0;
+Mesh.VolumeEdges = 0;
+PostProcessing.NbViews = 2;
+View[0].FileName = "output_sigma/salinity/salinity-000018/salinity-000018_COMP_0.msh";
+View[0].GeneralizedRaiseX = "0";
+View[0].GeneralizedRaiseY = "0";
+View[0].GeneralizedRaiseZ = "v0";
+View[0].Name = "salinity";
+View[0].GeneralizedRaiseFactor = 500;
+View[0].GeneralizedRaiseView = 1;
+View[0].Max = 35.00406862767804;
+View[0].MaxVisible = 35;
+View[0].MaxX = 30000;
+View[0].MaxY = 200;
+View[0].Min = -3.751830043999003;
+View[0].MinVisible = 35;
+View[0].MinX = -30000;
+View[0].MinY = -200;
+View[0].MinZ = -10000;
+View[0].NbTimeStep = 19;
+View[0].ShowElement = 1;
+View[0].Time = 0;
+View[0].TransformZZ = 0;
+View[0].UseGeneralizedRaise = 1;
+View[1].FileName = "output_sigma/z/z-000018/z-000018_COMP_0.msh";
+View[1].Name = "z";
+View[1].Max = 0.2580902842766859;
+View[1].MaxX = 30000;
+View[1].MaxY = 200;
+View[1].Min = -20;
+View[1].MinVisible = -20;
+View[1].MinX = -30000;
+View[1].MinY = -200;
+View[1].MinZ = -10000;
+View[1].NbTimeStep = 19;
+View[1].Time = 0;
+View[1].Visible = 0;

benchmarks/swe3d/rofiAdapt/prepro.py

+import slimPre
+import numpy as np
+import math
+
+data_dir = 'data/'
+slimPre.make_directory(data_dir)
+
+### Generate Mesh ###
+from dgpy.scripts import Common
+Common.genMesh("box.geo", 2)
+
+mesh_file = 'box.msh'
+
+print('Extruding mesh')
+def shiftOperation(node, iPerBound) :
+  n = [node[0], node[1] - 400, node[2]]
+  return n
+cutTags = ["cut"]
+pasteTags = ["paste"]
+mapFilename = data_dir+"periodicMesh.txt"
+periodicity = (shiftOperation, cutTags, pasteTags, mapFilename)
+
+nPart = 1
+if nPart > 1:
+    slimPre.dgpy.dgMeshPartition(mesh_file, nPart)
+    mesh_file = mesh_file[:-4] + '_' + str(nPart) + '.msh'
+
+mesh2d = slimPre.Mesh(mesh_file)
+region_global = slimPre.Region(mesh2d)
+xyz = region_global.coordinates
+bath = np.where(xyz[:,0] <=-2e4, 2,
+        np.where(xyz[:,0] < 2e4, 11 +  9 * np.sin( (xyz[:,0]/2e4 * np.pi/2) ),
+        20))
+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', 'bath')
+
+#slimPre.extrude(mesh_file, (data_dir+'bath_2d.nc','bath'), nb_layers=int(10), mesh_file_name_out=data_dir+'mesh3d.msh', factor_show=500, periodicity=periodicity)
+zLayers = [.5 * i for i in range(4)]
+zLayers += [1 * i for i in range(2,100)]
+print(zLayers)
+slimPre.extrude(mesh_file, (data_dir+'bath_2d.nc','bath'), z_layers=zLayers, mesh_file_name_out=data_dir+'mesh3d.msh', factor_show=200, periodicity=periodicity)
+
+slimPre.write_file(data_dir+'open_bnd.nc', region=None, time=None, data=[('u',.5), ('v',0), ('Sriv', 0), ('Ssea', 35)])
+
+
+
+print('preprocessing done')
+slimPre.exit(0)

benchmarks/swe3d/rofiAdapt/rofi.py

+import slim3d
+from slimPre import make_directory
+import shutil
+
+output_dir = 'output/'
+data_dir = 'data/'
+make_directory(output_dir)
+shutil.copyfile(data_dir+'mesh3d.msh', output_dir+'mesh3d.msh')
+shutil.copyfile(data_dir+'mesh3d_show.msh', output_dir+'mesh3d_show.msh')
+
+
+domain = slim3d.Domain(data_dir+'mesh3d.msh', data_dir+'periodicMesh.txt')
+
+equations = slim3d.Slim3d_equations(domain, temperature=False, salinity=True)
+equations.set_implicit_vertical(True)
+#equations.set_vertical_viscosity('gotm')
+#equations.set_vertical_diffusivity('gotm')
+equations.set_boundary_open(['river'], u=(data_dir+'open_bnd.nc', 'u'), v=(data_dir+'open_bnd.nc', 'v'), salinity=(data_dir+'open_bnd.nc', 'Sriv'))
+equations.set_boundary_open(['open'], salinity=(data_dir+'open_bnd.nc', 'Ssea'))
+equations.set_bottom_friction(False)
+#equations.set_lax_friedrichs_factor(0.05)
+equations.set_limiter(True)
+equations.set_initial_temperature('vertical_gradient', None, 20, 0)
+equations.set_initial_salinity('vertical_gradient', None, 35, 0.)
+equations.set_vertical_adaptation(tau=200, uv_factor=0, rho_factor=1, minimum_height=.1, maximum_height=15, resize_factor=3, background_error=1e-4)
+#equations.set_vertical_adaptation(tau=5, minimum_height=.1, maximum_height=15, resize_factor=3, background_error=1e-3)
+
+
+
+
+time_loop = slim3d.Loop(equations, 
+        time_step=60, 
+        export_time_step=300, 
+        final_time=86400, 
+        output_directory=output_dir)
+time_loop.export_elevation()
+time_loop.export_salinity()
+time_loop.export_uv(False)
+time_loop.export_w()
+time_loop.export_z_coordinate()
+time_loop.export_uv2d(False)
+
+time_loop.loop()
+#time_loop.setup()
+#while time_loop.get_time() < time_loop.final_time:
+#    time_loop.advance_one_time_step()
+#    time_loop.check_sanity()
+#    #print('******************')
+#    #print(time_loop.equations._slimSolver.getUseConservativeALE())
+#    if time_loop.check_export():
+#        time_loop.print_iter_info()
+#        [relVolErr, relSErr, relTErr] = time_loop.check_mass_conservation()
+#        [absSDev, absTDev] = time_loop.check_tracer_consistency()
+#        time_loop.export_fields()
+#time_loop.terminate()

benchmarks/swe3d/rofiAdapt/show.sh

+#!/bin/bash
+
+odir=output
+#gmsh $odir/mesh3d_show.msh $odir/uv/uv_COMP_0.idx $odir/z/z.idx opt.opt
+gmsh $odir/mesh3d_show.msh $odir/salinity/salinity.idx $odir/z/z.idx opt.opt