diff --git a/docs/configuration.md b/docs/configuration.md index 3675fbc..8f7774a 100644 --- a/docs/configuration.md +++ b/docs/configuration.md @@ -63,6 +63,7 @@ str(receptors) | -------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `met_path` | Absolute path to ARL compatible meteorological data files | | `met_file_format` | String detailing file naming convention for meteorological data files using a mixture of datetime and regex syntax. The formatting string accepts `grep` compatible regular expressions (`.\*.arl`), `strftime` compatible datetime strings (`%Y%m%d%H`) or any combination of the two. Datetime syntax is expanded to all unique combinations required for the receptor and simulation duration and the intersection between the requested files and files available in `met_path` is determined with `grep`, allowing partial matching and compatible regular expressions to be used to identify the relevant data. Matching does not require the full format to be specified - e.g. `\*.arl`, `%Y`, `%Y%m%d`, `%Y%m%d_d0.*.arl` would all match with a file named `20180130_d01.arl`. | +| `n_hours_per_met_file` | Number of hours per meteorological data file. To determine the number of hours in an ARL compatible meteorological data file, refer to the README, including the file naming convention, provided by the data source. For example, the [NOAA HRRR README](https://www.ready.noaa.gov/data/archives/hrrr/README.TXT) specifies a "6 hour data file beginning with 00z - 05z in the first file of the day". Defaults to 6 | | `met_subgrid_buffer` | Percent to extend footprint area for meteorological subdomain when using `met_subgrid_enable`. Defaults to 0.1 (10%) | | `met_subgrid_enable` | Enables extraction of spatial subdomains from files in `met_path` using HYSPLIT's `xtrct_grid` binary prior to executing simulations. If enabled, will create files in `/met/`. This can substantially accelerate simulation speed at the cost of increased disk usage. Defaults to disabled | | `met_subgrid_levels` | If set, extracts the defined number of vertical levels from the meteorological data files to further accelerate simulations. Defaults to `NA`, which includes all vertical levels available | diff --git a/r/run_stilt.r b/r/run_stilt.r index 5b77282..49cfcd5 100755 --- a/r/run_stilt.r +++ b/r/run_stilt.r @@ -51,6 +51,7 @@ yres <- xres # Meteorological data input met_path <- '' met_file_format <- '%Y%m%d.%Hz.hrrra' +n_hours_per_met_file <- 6 met_subgrid_buffer <- 0.2 met_subgrid_enable <- F met_subgrid_levels <- NA @@ -239,6 +240,7 @@ stilt_apply(FUN = simulation_step, met_subgrid_levels = met_subgrid_levels, mgmin = mgmin, n_hours = n_hours, + n_hours_per_met_file = n_hours_per_met_file, n_met_min = n_met_min, ncycl = ncycl, ndump = ndump, diff --git a/r/src/find_met_files.r b/r/src/find_met_files.r index 18aa5d7..96f541d 100644 --- a/r/src/find_met_files.r +++ b/r/src/find_met_files.r @@ -1,42 +1,61 @@ #' find_met_files searches for meteorological data files -#' @author Ben Fasoli +#' @author Ben Fasoli & James Mineau #' #' Searches for available meteorological files matching the given strftime #' compatible file naming convention #' #' @param t_start time of simulation start +#' @param n_hours number of hours to run each simulation; negative indicates +#' backward in time +#' @param n_hours_per_met_file number of hours of meteorological data in each +#' met file #' @param met_file_format grep compatible file naming convention to identify #' meteorological data files necessary for the timing of the simulation #' indicated by \code{t_start} and \code{n_hours} -#' @param n_hours number of hours to run each simulation; negative indicates -#' backward in time #' @param met_path directory to find meteorological data #' #' @import dplyr #' @export -find_met_files <- function(t_start, met_file_format, n_hours, met_path) { +find_met_files <- function(t_start, n_hours, n_hours_per_met_file, + met_file_format, met_path) { require(dplyr) - + + ts <- as.POSIXct(t_start, tz = 'UTC') is_backward <- n_hours < 0 - - # TODO: implement n_hours_per_met_file to better determine file names at - # varying time resolutions - request <- as.POSIXct(t_start, tz='UTC') %>% - c(. + c(1, -1, n_hours, is_backward * (n_hours - 5)) * 3600) %>% - range() %>% - (function(x) seq(x[1], x[2], by = 'hour')) %>% - strftime(tz = 'UTC', format = met_file_format) - + met_bracket <- n_hours_per_met_file - 1 # ts can be in the middle of a met file + + # Generate the hours to search for + if (is_backward) { + met_hours <- seq( + ts - as.difftime(abs(n_hours) + met_bracket, units = 'hours'), + ts, + by = 3600 + ) + } else { + met_hours <- seq( + ts - as.difftime(met_bracket, units = 'hours'), + ts + as.difftime(n_hours, units = 'hours'), + by = 3600 + ) + } + + # Format the request and remove duplicates + request <- met_hours %>% + strftime(tz = 'UTC', format = met_file_format) %>% + unique() + + # Find the available files available <- dir(met_path, full.names = T, recursive = T) available <- available[!grepl('.lock', available)] - + + # Find the files that match the request idx <- do.call(c, lapply(request, function(pattern) { grep(pattern = pattern, x = available) })) - + if (any(idx < 1)) return() - - unique(available[idx]) + + unique(available[idx]) # Available files that match the request } diff --git a/r/src/simulation_step.r b/r/src/simulation_step.r index 40270e1..425874a 100644 --- a/r/src/simulation_step.r +++ b/r/src/simulation_step.r @@ -61,6 +61,7 @@ simulation_step <- function(before_footprint = list(function() {output}), mgmin = 10, mhrs = 9999, n_hours = -24, + n_hours_per_met_file = 6, n_met_min = 1, ncycl = 0, ndump = 0, @@ -257,7 +258,8 @@ simulation_step <- function(before_footprint = list(function() {output}), link_files(exe, rundir) # Find necessary met files - met_files <- find_met_files(r_run_time, met_file_format, n_hours, met_path) + met_files <- find_met_files(r_run_time, n_hours, n_hours_per_met_file, + met_file_format, met_path) if (length(met_files) < n_met_min) { msg <- paste('Insufficient number of meteorological files found. Check', 'specifications in run_stilt.r') @@ -265,25 +267,26 @@ simulation_step <- function(before_footprint = list(function() {output}), cat(msg, '\n', file = file.path(rundir, 'stilt.log'), append = T) return() } - + if (met_subgrid_enable) { met_path <- file.path(output_wd, 'met') calc_met_subgrids(met_files, met_path, exe, projection, xmn, xmx, ymn, ymx, levels = met_subgrid_levels, met_subgrid_buffer = met_subgrid_buffer) + + # Find necessary met files for subgrids + met_files <- find_met_files(r_run_time, n_hours, n_hours_per_met_file, + met_file_format, met_path) + if (length(met_files) < n_met_min) { + msg <- paste('Insufficient number of meteorological files found. Check', + 'specifications in run_stilt.r') + warning(msg) + cat(msg, '\n', file = file.path(rundir, 'stilt.log'), append = T) + return() + } } - - # Find necessary met files - met_files <- find_met_files(r_run_time, met_file_format, n_hours, met_path) - if (length(met_files) < n_met_min) { - msg <- paste('Insufficient number of meteorological files found. Check', - 'specifications in run_stilt.r') - warning(msg) - cat(msg, '\n', file = file.path(rundir, 'stilt.log'), append = T) - return() - } - + # Execute particle trajectory simulation, and read results into data frame output$receptor <- list(run_time = r_run_time, lati = r_lati, diff --git a/r/stilt_cli.r b/r/stilt_cli.r index 9a18ce8..a7d560d 100755 --- a/r/stilt_cli.r +++ b/r/stilt_cli.r @@ -125,6 +125,7 @@ stilt_args <- list( met_subgrid_levels = as.numeric(args$met_subgrid_levels), mgmin = as.numeric(args$mgmin), n_hours = as.numeric(args$n_hours), + n_hours_per_met_file = as.numeric(args$n_hours_per_met_file), n_met_min = as.numeric(args$n_met_min), ncycl = as.numeric(args$ncycl), ndump = as.numeric(args$ndump),