From 8e65b791b6722951758c84c757c832958d0ef5a0 Mon Sep 17 00:00:00 2001
From: Johannes Boog <johannesboog@yahoo.de>
Date: Mon, 18 Oct 2021 17:03:12 +0200
Subject: [PATCH] [docs] examples polished
unused examples removed
examples that are described in vignettes removed
---
inst/examples/Theis_problem/theis_problem.R | 33 -------------
.../Theis_well_pumping/theis_well_pumping.R | 34 --------------
inst/examples/workflow_demos/ensemble.R | 46 -------------------
.../workflow_demos/read_from_benchmark.R | 8 ++--
.../benchmarks/theis_well_pumping/theis.prj | 2 +-
5 files changed, 4 insertions(+), 119 deletions(-)
delete mode 100644 inst/examples/Theis_problem/theis_problem.R
delete mode 100644 inst/examples/Theis_well_pumping/theis_well_pumping.R
delete mode 100644 inst/examples/workflow_demos/ensemble.R
diff --git a/inst/examples/Theis_problem/theis_problem.R b/inst/examples/Theis_problem/theis_problem.R
deleted file mode 100644
index a27e287..0000000
--- a/inst/examples/Theis_problem/theis_problem.R
+++ /dev/null
@@ -1,33 +0,0 @@
-
-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$new(sim_name = "axisym_theis",
- sim_path = "D:/OGS_Sim/")
-
-
-#===== Read in benchmark file =====
-
-# Modify the prj_path depending on where you saved the benchmark file.
-prj_path <- "inst/extdata/benchmarks/AxiSymTheis/axisym_theis.prj"
-
-# Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path, T)
-
-
-#===== Run simulation =====
-
-
-e <- run_simulation(ogs6_obj)
diff --git a/inst/examples/Theis_well_pumping/theis_well_pumping.R b/inst/examples/Theis_well_pumping/theis_well_pumping.R
deleted file mode 100644
index d40df19..0000000
--- a/inst/examples/Theis_well_pumping/theis_well_pumping.R
+++ /dev/null
@@ -1,34 +0,0 @@
-
-library(r2ogs6)
-
-
-#===== Set up simulation object =====
-
-
-# First make sure you're ready to go by setting r2ogs6.default_ogs_bin_path.
-# You can do this by commenting out the line below and modifying the path to
-# fit your system.
-
-# options("r2ogs6.default_ogs_bin_path" = "your_path_here")
-
-
-# Then we can create a simulation object.
-
-ogs6_obj <- OGS6$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)
diff --git a/inst/examples/workflow_demos/ensemble.R b/inst/examples/workflow_demos/ensemble.R
deleted file mode 100644
index c306bc5..0000000
--- a/inst/examples/workflow_demos/ensemble.R
+++ /dev/null
@@ -1,46 +0,0 @@
-
-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$run_simulation(parallel = TRUE)
-
diff --git a/inst/examples/workflow_demos/read_from_benchmark.R b/inst/examples/workflow_demos/read_from_benchmark.R
index b067d2a..c2259e1 100644
--- a/inst/examples/workflow_demos/read_from_benchmark.R
+++ b/inst/examples/workflow_demos/read_from_benchmark.R
@@ -13,9 +13,9 @@ library(r2ogs6)
# Then we can create a simulation object.
-
+tmpdir <- tempdir()
ogs6_obj <- OGS6$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)
diff --git a/inst/extdata/benchmarks/theis_well_pumping/theis.prj b/inst/extdata/benchmarks/theis_well_pumping/theis.prj
index d4653df..b7877db 100644
--- a/inst/extdata/benchmarks/theis_well_pumping/theis.prj
+++ b/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>
--
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