From ee1e6923b3c5e73dbe2622107b3af8927a5a655c Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Tue, 24 Nov 2020 09:24:21 +0100
Subject: [PATCH] [structure] Moved examples folder to inst directory since
it's not a standard top level directory
---
inst/examples/read_from_benchmark_example.R | 32 +++
inst/examples/square_1x1_quad8_1e2.vtu | 33 +++
inst/examples/user_input_example.R | 235 ++++++++++++++++++++
3 files changed, 300 insertions(+)
create mode 100644 inst/examples/read_from_benchmark_example.R
create mode 100644 inst/examples/square_1x1_quad8_1e2.vtu
create mode 100644 inst/examples/user_input_example.R
diff --git a/inst/examples/read_from_benchmark_example.R b/inst/examples/read_from_benchmark_example.R
new file mode 100644
index 0000000..19bbc55
--- /dev/null
+++ b/inst/examples/read_from_benchmark_example.R
@@ -0,0 +1,32 @@
+detach("package:r2ogs6", unload=TRUE)
+library(r2ogs6)
+
+
+#This is where the user defines their data.
+
+#============================== SET UP SIMULATION OBJECT ================================
+
+#If you want to test this, don't forget to alter the ogs_bin_path to fit your installation location!
+
+#First, we need to create a simulation object.
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim",
+ sim_id = 1,
+ sim_path = "D:\\OGS_Sim\\",
+ ogs_bin_path = "D:\\Programme\\OpenGeoSys\\ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils\\bin\\")
+
+#============================== READ IN .prj FILE ================================
+
+#This will only work if the working directory is r2ogs6, but is fine for testing purposes.
+prj_path <- paste0("inst/extdata/flow_free_expansion/flow_free_expansion.prj")
+
+#prj_path = paste0("D:\\Programme\\OpenGeoSys\\ogs-master-Tests-Data-HydroMechanics\\",
+# "Tests\\Data\\HydroMechanics\\IdealGas\\flow_no_strain\\flow_no_strain.prj")
+
+read_in_prj(ogs6_obj, prj_path)
+
+#============================== Execution ================================
+
+#Calls ogs6 object validator functions, exports all necessary files and starts OpenGeoSys6
+
+run_simulation(ogs6_obj)
diff --git a/inst/examples/square_1x1_quad8_1e2.vtu b/inst/examples/square_1x1_quad8_1e2.vtu
new file mode 100644
index 0000000..32a0c26
--- /dev/null
+++ b/inst/examples/square_1x1_quad8_1e2.vtu
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+ <UnstructuredGrid>
+ <Piece NumberOfPoints="341" NumberOfCells="100">
+ <PointData>
+ </PointData>
+ <CellData>
+ </CellData>
+ <Points>
+ <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.4142135624">
+ AQAAAACAAAD4HwAAAwQAAA==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
+ </DataArray>
+ </Points>
+ <Cells>
+ <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="340">
+ AQAAAACAAAAAGQAAuwQAAA==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
+ </DataArray>
+ <DataArray type="Int64" Name="offsets" format="binary" RangeMin="8" RangeMax="800">
+ AQAAAACAAAAgAwAApgAAAA==eJwtxRFghAAAAMC2SRiGYRg+huFjGIZhGIZh+BiGYRiGYfgYhoPu5MLgETl24tSZX85d+O3SlWs3bt259+DRH0+evXj15t2HT399+Xbw8xQ6cuzEqTO/nLvw26Ur127cunPvwaM/njx78erNuw+f/vry7eD3KXTk2IlTZ345d+G3S1eu3bh1596DR388efbi1Zt3Hz799eXbwd9T6MixE/8DLbMvQA==
+ </DataArray>
+ <DataArray type="UInt8" Name="types" format="binary" RangeMin="23" RangeMax="23">
+ AQAAAACAAABkAAAADAAAAA==eJwTF6c9AADGKQj9
+ </DataArray>
+ <DataArray type="Int64" Name="faces" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAAAgAwAAEAAAAA==eJxjYBgFo2AU4AIAAyAAAQ==
+ </DataArray>
+ <DataArray type="Int64" Name="faceoffsets" format="binary" RangeMin="1" RangeMax="100">
+ AQAAAACAAAAgAwAArwAAAA==eJwtxdciAgAAAEAjkYRskazskpUtFJGRUbYI//8NHrp7ueamhha3OuA2B93uDofc6bC7HHG3e9zrqPvc7wEPesjDHvGoYx7zuOOecMKTnvK0ZzzrpOc87wUvesnLXnHKaa864zWve8Ob3nLW297xrve87wMf+sg5H/vEp8674DOfu+gLX7rkK1/7xrcu+873fvCjK676yc9+8avf/O4Pf7rmL3+77h//+s//+ewTuw==
+ </DataArray>
+ </Cells>
+ </Piece>
+ </UnstructuredGrid>
+</VTKFile>
diff --git a/inst/examples/user_input_example.R b/inst/examples/user_input_example.R
new file mode 100644
index 0000000..89546b7
--- /dev/null
+++ b/inst/examples/user_input_example.R
@@ -0,0 +1,235 @@
+detach("package:r2ogs6", unload=TRUE)
+library(r2ogs6)
+
+
+#This is where the user defines their data.
+
+#============================== SET UP SIMULATION OBJECT ================================
+
+#If you want to test this, don't forget to alter the paths to fit your system!
+
+#First, we need to create a simulation object.
+
+ogs6_obj <- OGS6$new(sim_name = "my_sim",
+ sim_id = 1,
+ sim_path = "D:\\OGS_Sim\\",
+ ogs_bin_path = "D:\\Programme\\OpenGeoSys\\ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils\\bin\\")
+
+
+#============================== ADD .gml DATA ================================
+
+#(source: HydroComponent Benchmarks -> IdealGas -> flow_no_strain -> square_1x1.gml)
+
+#Add some geometry
+input_add(r2ogs6_gml(name = "square_1x1_geometry",
+ points = tibble::tibble(x = c(0, 0, 1, 1),
+ y = c(0, 1, 0, 1),
+ z = c(0, 0, 0, 0),
+ name = c("origin", rep("", 3))),
+ polylines = list(list(name = "left", c(0, 1)),
+ list(name = "right", c(2, 3)),
+ list(name = "bottom", c(0, 2)),
+ list(name = "top", c(1, 3)))),
+ ogs6_obj)
+
+#============================== ADD .vtu DATA ================================
+
+#Let's add our data for the .vtk file, which contains information about our mesh.
+
+# #This calls an external script (which is why we needed to specify some paths earlier)
+# generate_structured_mesh(ogs6_obj, "-e quad --lx 1 --ly 1 --lz 1")
+
+#To make sure our geometry is right, let's copy the .vtu from the benchmark
+# we're trying to reverse engineer...
+
+pick_vtu_file(ogs6_obj)
+
+
+#============================== ADD .prj DATA ================================
+
+#Let's add our data for the .prj file, arguably the most important file.
+#(source: HydroComponent Benchmarks -> IdealGas -> flow_no_strain -> flow_no_strain.prj)
+
+#We need:
+#1. Either one mesh and one geometry file OR multiple mesh files (for the latter case: Skip to
+# previous part and call generate_structured_mesh at least one more time)
+
+#2. One or more process elements:
+input_add(r2ogs6_process(name = "HM",
+ type = "HYDRO_MECHANICS",
+ integration_order = 3,
+ dimension = 2,
+ constitutive_relation = c(type = "LinearElasticIsotropic",
+ youngs_modulus = "E",
+ poissons_ratio = "nu"),
+ process_variables = c(displacement = "displacement",
+ pressure = "pressure"),
+ secondary_variables = list(c("sigma_xx", "sigma_xx"),
+ c("sigma_yy", "sigma_yy"),
+ c("sigma_zz", "sigma_zz"),
+ c("sigma_xy", "sigma_xy"),
+ c("epsilon_xx", "epsilon_xx"),
+ c("epsilon_yy", "epsilon_yy"),
+ c("epsilon_zz", "epsilon_zz"),
+ c("epsilon_xy", "epsilon_xy"),
+ c("velocity", "velocity")),
+ specific_body_force = c(0, 0)),
+ ogs6_obj)
+
+#3. One time_loop element:
+input_add(r2ogs6_time_loop(processes = list(r2ogs6_tl_process(ref = "HM",
+ nonlinear_solver = "basic_newton",
+ convergence_criterion = list(type = "PerComponentDeltaX",
+ norm_type = "NORM2",
+ reltols = "5e-8 1e10 1e10"),
+ time_discretization = list(type = "BackwardEuler"),
+ time_stepping = list(type = "FixedTimeStepping",
+ t_initial = 0,
+ t_end = 100,
+ timesteps = list(pair = list(rep = 1,
+ delta_t = 0.1))
+ )
+ )),
+ output = r2ogs6_tl_output(type = "VTK",
+ prefix = "flow_no_strain_pcs_{:process_id}",
+ suffix = "_ts_{:timestep}_t_{:time}",
+ timesteps = list(pair = list(rep = 1,
+ each_steps = 1000)),
+ variables = list("displacement",
+ "pressure",
+ "sigma_xx",
+ "sigma_yy",
+ "sigma_zz",
+ "sigma_xy",
+ "epsilon_xx",
+ "epsilon_yy",
+ "epsilon_zz",
+ "epsilon_xy",
+ "velocity"))),
+ ogs6_obj)
+
+#4. One or more medium elements:
+input_add(r2ogs6_medium(phases = list(r2ogs6_medium_phase(type = "Gas",
+ properties = list(r2ogs6_medium_property(name = "viscosity",
+ type = "Constant",
+ value = 1e-5),
+ r2ogs6_medium_property(name = "density",
+ type = "IdealGasLaw"),
+ r2ogs6_medium_property(name = "molar_mass",
+ type = "Constant",
+ value = 0.028964397787206768))),
+ r2ogs6_medium_phase(type = "Solid",
+ properties = list(r2ogs6_medium_property(name = "porosity",
+ type = "Constant",
+ value = 0.03),
+ r2ogs6_medium_property(name = "density",
+ type = "Constant",
+ value = 2.17e3),
+ r2ogs6_medium_property(name = "biot_coefficient",
+ type = "Constant",
+ value = 0.6)))),
+ properties = list(r2ogs6_medium_property(name = "reference_temperature",
+ type = "Constant",
+ value = 293.15),
+ r2ogs6_medium_property(name = "permeability",
+ type = "Constant",
+ value = 1e-4))),
+ ogs6_obj)
+
+#5. One or more parameters:
+input_add(r2ogs6_parameter(name = "E",
+ type = "Constant",
+ values = 1e9),
+ ogs6_obj)
+
+input_add(r2ogs6_parameter(name = "nu",
+ type = "Constant",
+ values = .3),
+ ogs6_obj)
+
+input_add(r2ogs6_parameter(name = "displacement0",
+ type = "Constant",
+ values = c(0, 0)),
+ ogs6_obj)
+
+input_add(r2ogs6_parameter(name = "pressure0",
+ type = "Constant",
+ values = 1e5),
+ ogs6_obj)
+
+input_add(r2ogs6_parameter(name = "zero",
+ type = "Constant",
+ values = 0),
+ ogs6_obj)
+
+input_add(r2ogs6_parameter(name = "flux",
+ type = "Constant",
+ values = 1e-3),
+ ogs6_obj)
+
+
+#6. One or more process variables
+input_add(r2ogs6_process_variable(name = "displacement",
+ components = 2,
+ order = 2,
+ initial_condition = "displacement0",
+ boundary_conditions = list(r2ogs6_boundary_condition(type = "Dirichlet",
+ parameter = "zero",
+ component = 0,
+ geometrical_set = "square_1x1_geometry",
+ geometry = "left"),
+ r2ogs6_boundary_condition(type = "Dirichlet",
+ parameter = "zero",
+ component = 1,
+ geometrical_set = "square_1x1_geometry",
+ geometry = "bottom"),
+ r2ogs6_boundary_condition(type = "Dirichlet",
+ parameter = "zero",
+ component = 0,
+ geometrical_set = "square_1x1_geometry",
+ geometry = "right"),
+ r2ogs6_boundary_condition(type = "Dirichlet",
+ parameter = "zero",
+ component = 1,
+ geometrical_set = "square_1x1_geometry",
+ geometry = "top"))),
+ ogs6_obj)
+
+input_add(r2ogs6_process_variable(name = "pressure",
+ components = 1,
+ order = 1,
+ initial_condition = "pressure0",
+ boundary_conditions = list(r2ogs6_boundary_condition(type = "Neumann",
+ parameter = "flux",
+ component = 0,
+ geometrical_set = "square_1x1_geometry",
+ geometry = "left")
+ )
+ ),
+ ogs6_obj)
+
+#7. One or more nonlinear solvers
+input_add(r2ogs6_nonlinear_solver(name = "basic_newton",
+ type = "Newton",
+ max_iter = 50,
+ linear_solver = "general_linear_solver"),
+ ogs6_obj)
+
+#8. One or more linear solvers
+input_add(r2ogs6_linear_solver(name = "general_linear_solver",
+ eigen = list(solver_type = "BiCGSTAB",
+ precon_type = "ILUT",
+ max_iteration_step = 10000,
+ error_tolerance = 1e-16),
+ lis = "-i bicgstab -p ilu -tol 1e-16 -maxiter 10000"),
+ ogs6_obj)
+
+
+#OPTIONAL: A test definition
+
+#============================== Execution ================================
+
+#Calls ogs6 object validator functions, exports all necessary files and starts OpenGeoSys6
+
+run_simulation(ogs6_obj)
+
--
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