From b38055278d4a801598ece9d2c93716a9bf67134a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 27 Jan 2017 01:00:07 +0100 Subject: 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 --- man/FOCUS_GW_scenarios_2012.Rd | 9 ++++++++- man/FOCUS_PELMO_crop_sze_names.Rd | 20 ++++++++++++++++++++ man/FOCUS_PELMO_crops.Rd | 21 +++++++++++++++++++++ man/FOCUS_PELMO_location_codes.Rd | 18 ++++++++++++++++++ man/PELMO_path.Rd | 18 ++++++++++++++++++ man/PELMO_runs.Rd | 35 +++++++++++++++++++++++++++++++++++ man/create_run_list.Rd | 22 ++++++++++++++++++++++ man/run_PELMO.Rd | 27 +++++++++++++++++++++++++++ 8 files changed, 169 insertions(+), 1 deletion(-) create mode 100644 man/FOCUS_PELMO_crop_sze_names.Rd create mode 100644 man/FOCUS_PELMO_crops.Rd create mode 100644 man/FOCUS_PELMO_location_codes.Rd create mode 100644 man/PELMO_path.Rd create mode 100644 man/PELMO_runs.Rd create mode 100644 man/create_run_list.Rd create mode 100644 man/run_PELMO.Rd (limited to 'man') diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd index f2417d9..a19bbe5 100644 --- a/man/FOCUS_GW_scenarios_2012.Rd +++ b/man/FOCUS_GW_scenarios_2012.Rd @@ -1,10 +1,16 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/FOCUS_GW_scenarios_2012.R +\docType{data} \name{FOCUS_GW_scenarios_2012} \alias{FOCUS_GW_scenarios_2012} \title{A very small subset of the FOCUS Groundwater scenario defitions} +\format{An object of class \code{list} of length 2.} +\usage{ +FOCUS_GW_scenarios_2012 +} \description{ -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). } \examples{ FOCUS_GW_scenarios_2012 @@ -14,3 +20,4 @@ FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 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 } +\keyword{datasets} diff --git a/man/FOCUS_PELMO_crop_sze_names.Rd b/man/FOCUS_PELMO_crop_sze_names.Rd new file mode 100644 index 0000000..180c011 --- /dev/null +++ b/man/FOCUS_PELMO_crop_sze_names.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FOCUS_PELMO_data.R +\docType{data} +\name{FOCUS_PELMO_crop_sze_names} +\alias{FOCUS_PELMO_crop_sze_names} +\title{FOCUS PELMO crop acronyms used for naming sceneario files} +\format{An object of class \code{character} of length 25.} +\usage{ +FOCUS_PELMO_crop_sze_names +} +\description{ +A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 +for naming the .sze files located in the FOCUS directory. The crop acronyms +in the file names are sometimes capitalized, sometimes not. The scenario +files used for Beans (field) and Beans (vegetable) are the same. +} +\examples{ +print(FOCUS_PELMO_crop_sze_names) +} +\keyword{datasets} diff --git a/man/FOCUS_PELMO_crops.Rd b/man/FOCUS_PELMO_crops.Rd new file mode 100644 index 0000000..f6a41b4 --- /dev/null +++ b/man/FOCUS_PELMO_crops.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FOCUS_PELMO_data.R +\docType{data} +\name{FOCUS_PELMO_crops} +\alias{FOCUS_PELMO_crops} +\title{FOCUS PELMO crop names} +\format{An object of class \code{character} of length 25.} +\usage{ +FOCUS_PELMO_crops +} +\description{ +A named character vector with the crop names used in the PELMO 5.5.3 GUI. +For the names, three letter codes were constructed by generally taking the +first three letters in lower case. Only when there is an expression in +parentheses, the first letter of this expression becomes the first letter +in the three letter code, i.e. 'Peas (animals)' has the code \code{ape}. +} +\examples{ +print(FOCUS_PELMO_crops) +} +\keyword{datasets} diff --git a/man/FOCUS_PELMO_location_codes.Rd b/man/FOCUS_PELMO_location_codes.Rd new file mode 100644 index 0000000..961a840 --- /dev/null +++ b/man/FOCUS_PELMO_location_codes.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FOCUS_PELMO_data.R +\docType{data} +\name{FOCUS_PELMO_location_codes} +\alias{FOCUS_PELMO_location_codes} +\title{Location codes in FOCUS PELMO} +\format{An object of class \code{character} of length 9.} +\usage{ +FOCUS_PELMO_location_codes +} +\description{ +A named character vector of one letter location codes used in FOCUS PELMO, +indexed by three letter acronyms. +} +\examples{ +print(FOCUS_PELMO_location_codes) +} +\keyword{datasets} diff --git a/man/PELMO_path.Rd b/man/PELMO_path.Rd new file mode 100644 index 0000000..e8ca50e --- /dev/null +++ b/man/PELMO_path.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{PELMO_path} +\alias{PELMO_path} +\title{Create a path of run directories as the PELMO GUI does} +\usage{ +PELMO_path(psm, crop, scenario) +} +\arguments{ +\item{psm}{The psm identifier} + +\item{crop}{The PELMO crop acronym} + +\item{scenario}{The scenario} +} +\description{ +Create a path of run directories as the PELMO GUI does +} diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd new file mode 100644 index 0000000..71fe6ef --- /dev/null +++ b/man/PELMO_runs.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{PELMO_runs} +\alias{PELMO_runs} +\title{Set up runs for FOCUS PELMO} +\usage{ +PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto", + execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE, + overwrite = FALSE) +} +\arguments{ +\item{runs}{A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in \code{\link{FOCUS_PELMO_crops}}, +that hold character vectors of three letter scenario acronyms +as used in \code{\link{FOCUS_GW_scenarios_2012}}.} + +\item{psm_dir}{The directory where the psm files are located} + +\item{version}{The FOCUS PELMO version} + +\item{PELMO_base}{Where the FOCUS PELMO installation is located} + +\item{execute}{Should PELMO be executed directly?} + +\item{cores}{The number of cores to execute PELMO runs in parallel} + +\item{evaluate}{Should the results be returned?} + +\item{overwrite}{Should an existing run directories be overwritten} +} +\description{ +Per default, the runs are also executed with FOCUS PELMO, and the results are processed +and returned. +} diff --git a/man/create_run_list.Rd b/man/create_run_list.Rd new file mode 100644 index 0000000..3151165 --- /dev/null +++ b/man/create_run_list.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{create_run_list} +\alias{create_run_list} +\title{Create a list of runs that we can traverse} +\usage{ +create_run_list(runs, psm_dir = ".", check_psm_files = FALSE) +} +\arguments{ +\item{runs}{A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in \code{\link{FOCUS_PELMO_crops}}, +that hold character vectors of three letter scenario acronyms +as used in \code{\link{FOCUS_GW_scenarios_2012}}.} + +\item{psm_dir}{The directory where the psm files are located} + +\item{check_psm_files}{Should we check if the psm file exists} +} +\description{ +Create a list of runs that we can traverse +} diff --git a/man/run_PELMO.Rd b/man/run_PELMO.Rd new file mode 100644 index 0000000..a286c5c --- /dev/null +++ b/man/run_PELMO.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{run_PELMO} +\alias{run_PELMO} +\title{Run PELMO} +\usage{ +run_PELMO(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto", + cores = getOption("mc.cores", 2L)) +} +\arguments{ +\item{runs}{A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in \code{\link{FOCUS_PELMO_crops}}, +that hold character vectors of three letter scenario acronyms +as used in \code{\link{FOCUS_GW_scenarios_2012}}.} + +\item{psm_dir}{The directory where the psm files are located} + +\item{version}{The FOCUS PELMO version} + +\item{PELMO_base}{Where the FOCUS PELMO installation is located} + +\item{cores}{The number of cores to execute PELMO runs in parallel} +} +\description{ +Run PELMO +} -- cgit v1.2.1