[docs] examples polished

    unused examples removed
    examples that are described in vignettes removed

inst/examples/Theis_problem/theis_problem.R

-
-library(r2ogs6)
-
-
-#===== Set up simulation object =====
-
-
-# First make sure you're ready to go by setting r2ogs6.default_ogs_bin_path.
-# You can do this by commenting out the line below and modifying the path to
-# fit your system.
-
-# options("r2ogs6.default_ogs_bin_path" = "your_path_here")
-
-
-# Then we can create a simulation object.
-
-ogs6_obj <- OGS6$new(sim_name = "axisym_theis",
-                     sim_path = "D:/OGS_Sim/")
-
-
-#===== Read in benchmark file =====
-
-# Modify the prj_path depending on where you saved the benchmark file.
-prj_path <- "inst/extdata/benchmarks/AxiSymTheis/axisym_theis.prj"
-
-# Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path, T)
-
-
-#===== Run simulation =====
-
-
-e <- run_simulation(ogs6_obj)

inst/examples/Theis_well_pumping/theis_well_pumping.R

-
-library(r2ogs6)
-
-
-#===== Set up simulation object =====
-
-
-# First make sure you're ready to go by setting r2ogs6.default_ogs_bin_path.
-# You can do this by commenting out the line below and modifying the path to
-# fit your system.
-
-# options("r2ogs6.default_ogs_bin_path" = "your_path_here")
-
-
-# Then we can create a simulation object.
-
-ogs6_obj <- OGS6$new(sim_name = "theis",
-                     sim_id = 1,
-                     sim_path = "D:/OGS_Sim/")
-
-
-#===== Read in benchmark file =====
-
-# Modify the prj_path depending on where you saved the benchmark file.
-prj_path <- "inst/extdata/benchmarks/theis_well_pumping/theis.prj"
-
-# Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path)
-
-
-#===== Run simulation =====
-
-
-e <- run_simulation(ogs6_obj)

inst/examples/workflow_demos/ensemble.R

-
-library(r2ogs6)
-
-
-#===== Set up simulation object =====
-
-
-# First make sure you're ready to go by setting r2ogs6.default_ogs_bin_path.
-# You can do this by commenting out the line below and modifying the path to
-# fit your system.
-
-# options("r2ogs6.default_ogs_bin_path" = "your_path_here")
-
-
-# Then we can create a simulation object.
-
-ogs6_obj <- OGS6$new(sim_name = "my_sim",
-                     sim_id = 1,
-                     sim_path = "D:/OGS_Sim/")
-
-
-#===== Read in benchmark file =====
-
-
-# Modify the prj_path depending on where you saved the benchmark file.
-prj_path <- "inst/extdata/flow_free_expansion/flow_free_expansion.prj"
-
-# Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path)
-
-
-#===== Create ensemble from simulation object =====
-
-
-ogs6_ens <- OGS6_Ensemble$new(
-    ogs6_obj = ogs6_obj,
-    parameters = list(list(ogs6_obj$parameters[[2]]$value, c(0.2, 0.3, 0.4)))
-)
-
-
-#===== Run simulation =====
-
-
-# Should work on machines with more RAM
-ogs6_ens$run_simulation(parallel = TRUE)
-

inst/examples/workflow_demos/read_from_benchmark.R

@@ -13,9 +13,9 @@ library(r2ogs6)
 
 
 # Then we can create a simulation object.
-
+tmpdir <- tempdir()
 ogs6_obj <- OGS6$new(sim_name = "flow_free_expansion",
-                     sim_path = "D:/OGS_Sim/")
+                     sim_path = tmpdir)
 
 
 #===== Read in benchmark file =====
@@ -24,10 +24,8 @@ ogs6_obj <- OGS6$new(sim_name = "flow_free_expansion",
 prj_path <- "inst/extdata/benchmarks/flow_free_expansion/flow_free_expansion.prj"
 
 # Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path)
+read_in_prj(ogs6_obj, prj_path, read_in_gml = T)
 
 
 #===== Run simulation =====
-
-
 e <- ogs6_run_simulation(ogs6_obj, write_logfile = FALSE)

inst/extdata/benchmarks/theis_well_pumping/theis.prj

@@ -34,7 +34,7 @@
                             <name>concentration</name>
                             <properties>
                                 <property>
-                                    <name>molecular_diffusion</name>
+                                    <name>pore_diffusion</name>
                                     <type>Constant</type>
                                     <value>2e-9</value>
                                 </property>