Set up FOCUS PELMO runs and run them in parallel

- This works on Linux using wine
- PELMO runs (including pelmo.inp files) are correctly generated
- The PLM files for FOCUS Pesticide_D in the test data archive are
  correctly reproduced
- The data files (including FOCUS groundwater scenario data) are now
  created and documented in R files

1 files changed, 60 insertions, 2 deletions

diff --git a/R/FOCUS_GW_scenarios_2012.R b/R/FOCUS_GW_scenarios_2012.R
index 49cf7dd..e26ea50 100644
--- a/R/FOCUS_GW_scenarios_2012.R
+++ b/R/FOCUS_GW_scenarios_2012.R
@@ -1,11 +1,69 @@
 #' A very small subset of the FOCUS Groundwater scenario defitions
 #' 
-#' Currently, only a small subset of the soil definitions are provided.
+#' Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The 
+#' soil definitions are from page 46ff. from FOCUS (2012).
 #' 
 #' @name FOCUS_GW_scenarios_2012
 #' @references FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. 
 #'  FOrum for the Co-ordination of pesticde fate models and their USe. 
 #'  http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
+#' @export
 #' @examples
 #' FOCUS_GW_scenarios_2012
-NULL
+FOCUS_GW_scenarios_2012 = list()
+
+n_layers = c(7, 6, 6, 5, 5, 6, 4, 6, 6)
+acronyms = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")
+FOCUS_GW_scenarios_2012$names = c("Ch\u00e2teaudun", "Hamburg", "Jokioinen",
+                                  "Kremsm\u00fcnster", "Okehampton",
+                                  "Piacenza", "Porto", "Sevilla", "Thiva")
+
+names(FOCUS_GW_scenarios_2012$names) = acronyms
+FOCUS_GW_scenarios_2012$soils <- data.frame(
+  location= rep(acronyms, times = n_layers),
+  horizon = c("Ap", "B1", "B2", "II C1", "II C1", "II C2", "M",
+              "Ap", "BvI", "BvII", "Bv/Cv", "Cv", "Cv",
+              "Ap", "Bs", "BC1", "BC2", "BC2", "Cg",
+              rep(NA, 5),
+              "A", "Bw1", "BC", "C", "C",
+              "Ap", "Ap", "Bw", "Bw", "2C", "2C",
+              rep(NA, 4),
+              rep(NA, 6),
+              "Ap1", "Ap2", "Bw", "Bw", "Ck1", "Ck1"),
+  number = unlist(sapply(n_layers, function(x) 1:x)),
+  pH_H2O = c(8.0, 8.1, 8.2, 8.5, 8.5, 8.5, 8.3,
+             6.4, 5.6, 5.6, 5.7, 5.5, 5.5,
+             6.2, 5.6, 5.4, 5.4, 5.4, 5.3,
+             7.7, 7.0, 7.1, 7.1, 7.1,
+             5.8, 6.3, 6.5, 6.6, 6.6,
+             7, 7, 6.3, 6.3, 6.4, 6.4,
+             4.9, 4.8, 4.8, 4.8,
+             7.3, 7.3, 7.8, 8.1, 8.1, 8.2,
+             7.7, 7.7, 7.8, 7.8, 7.8, 7.8),
+  perc_clay = c(30, 31, 25, 26, 26, 24, 31,
+                7.2, 6.7, 0.9, 0, 0, 0,
+                3.6, 1.8, 1.2, 1.7, 1.7, 1.9,
+                14, 25, 27, 27, 27,
+                18, 17, 14, 9, 9,
+                15, 15, 7, 7, 0, 0,
+                10, 8, 8, 8,
+                14, 13, 15, 16, 16, 22,
+                25.3, 25.3, 29.6, 31.9, 32.9, 32.9),
+  perc_oc = c(1.39, 0.93, 0.7, 0.3, 0.3, 0.27, 0.21,
+              1.5, 1, 0.2, 0, 0, 0,
+              4.06, 0.84, 0.36, 0.29, 0.29, 0.21,
+              3.6, 1.0, 0.5, 0.5, 0.5,
+              2.2, 0.7, 0.4, 0.1, 0.1,
+              1.26, 1.26, 0.47, 0.47, 0, 0,
+              1.42, 0.78, 0.78, 0.78,
+              0.93, 0.93, 0.70, 0.58, 0.58, 0.49,
+              0.74, 0.74, 0.57, 0.31, 0.18, 0.18),
+  rel_deg = c(1, 0.5, 0.5, 0.3, 0, 0, 0,
+              1, 0.5, 0.3, 0.3, 0.3, 0,
+              1, 0.5, 0.3, 0.3, 0, 0,
+              1, 0.5, 0.5, 0.3, 0,
+              1, 0.5, 0.3, 0.3, 0,
+              1, 0.5, 0.5, 0.3, 0.3, 0,
+              1, 0.5, 0.3, 0,
+              1, 1, 0.5, 0.3, 0, 0,
+              1, 0.5, 0.5, 0.3, 0.3, 0))