debug branch and testcase
This commit is contained in:
Marco De Lucia
parent
5f333fcb77
commit
fcfa45169d
@ -1,8 +1,8 @@
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## Time-stamp: "Last modified 2024-04-10 22:38:14 delucia"
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## Time-stamp: "Last modified 2024-04-11 15:28:06 delucia"
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## Compile the fortran code. On Linux, if a fortran compiler is
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## installed, it should work out of the box
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here <- getwd()
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setwd("/home/work/simR/Rphree/SpecSim/")
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system("R CMD SHLIB SS_Sim.f SS_Vario.f -o SSlib.so")
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dyn.load("SSlib.so")
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@ -10,11 +10,60 @@ dyn.load("SSlib.so")
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## Load the functions
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source("SS_Fun_sim.R")
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source("SS_Fun_vario.R")
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setwd(here)
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setwd("/home/work/simR/Rphree/NAAICE_tug_input/build")
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library(lattice)
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library(PoetUtils)
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PlotField2 <- function (data, grid, nx, ny, contour = TRUE, nlevels = 12, breaks,
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palette = "heat.colors", rev.palette = TRUE, scale = TRUE,
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plot.axes = TRUE, ...)
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{
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if (!missing(grid)) {
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xc <- unique(sort(grid$cell$XCOORD))
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yc <- unique(sort(grid$cell$YCOORD))
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nx <- length(xc)
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ny <- length(yc)
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if (!length(data) == nx * ny)
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stop("Wrong nx, ny or grid")
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}
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else {
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xc <- seq(1, nx)
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yc <- seq(1, ny)
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}
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z <- matrix(round(data, 6), ncol = nx, nrow = ny, byrow = TRUE)
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pp <- t(z[rev(seq(1, nrow(z))), ])
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if (missing(breaks)) {
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breaks <- pretty(data, n = nlevels)
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}
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breakslen <- length(breaks)
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colors <- do.call(palette, list(n = breakslen - 1))
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if (rev.palette)
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colors <- rev(colors)
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if (scale) {
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par(mfrow = c(1, 2))
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nf <- layout(matrix(c(1, 2), 1, 2, byrow = TRUE), widths = c(4,
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1))
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}
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par(las = 1, mar = c(5, 5, 3, 1))
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image(xc, yc, pp, las = 1, asp = 1, breaks = breaks, col = colors,
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axes = FALSE, ann = plot.axes, ...)
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if (plot.axes) {
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axis(1)
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axis(2)
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}
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if (contour)
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contour(unique(sort(xc)), unique(sort(yc)), pp, breaks = breaks,
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add = TRUE)
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if (scale) {
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par(las = 1, mar = c(5, 1, 5, 5))
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PlotImageScale(data, breaks = breaks, add.axis = FALSE,
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axis.pos = 4, col = colors)
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axis(4, at = breaks)
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}
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invisible(pp)
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}
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## generate a grid. At the moment it must be a cartesian square grid
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## with number of cells a power of two, e.g. 128, 256, ...
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@ -72,54 +121,6 @@ range(ax)
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range(ay)
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PlotField2 <- function (data, grid, nx, ny, contour = TRUE, nlevels = 12, breaks,
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palette = "heat.colors", rev.palette = TRUE, scale = TRUE,
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plot.axes = TRUE, ...)
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{
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if (!missing(grid)) {
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xc <- unique(sort(grid$cell$XCOORD))
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yc <- unique(sort(grid$cell$YCOORD))
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nx <- length(xc)
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ny <- length(yc)
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if (!length(data) == nx * ny)
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stop("Wrong nx, ny or grid")
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}
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else {
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xc <- seq(1, nx)
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yc <- seq(1, ny)
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}
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z <- matrix(round(data, 6), ncol = nx, nrow = ny, byrow = TRUE)
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pp <- t(z[rev(seq(1, nrow(z))), ])
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if (missing(breaks)) {
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breaks <- pretty(data, n = nlevels)
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}
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breakslen <- length(breaks)
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colors <- do.call(palette, list(n = breakslen - 1))
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if (rev.palette)
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colors <- rev(colors)
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if (scale) {
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par(mfrow = c(1, 2))
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nf <- layout(matrix(c(1, 2), 1, 2, byrow = TRUE), widths = c(4,
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1))
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}
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par(las = 1, mar = c(5, 5, 3, 1))
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image(xc, yc, pp, las = 1, asp = 1, breaks = breaks, col = colors,
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axes = FALSE, ann = plot.axes, ...)
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if (plot.axes) {
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axis(1)
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axis(2)
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}
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if (contour)
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contour(unique(sort(xc)), unique(sort(yc)), pp, breaks = breaks,
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add = TRUE)
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if (scale) {
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par(las = 1, mar = c(5, 1, 5, 5))
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PlotImageScale(data, breaks = breaks, add.axis = FALSE,
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axis.pos = 4, col = colors)
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axis(4, at = breaks)
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}
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invisible(pp)
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}
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PlotField2(log10(ax), nx=200, ny=200, contour = FALSE, xaxs="i", yaxs="i", nlevels=6, plot.axes = FALSE)
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@ -322,3 +323,125 @@ PlotField2((out$Cl), nx=nx, ny=ny, contour = FALSE, nlevels=10,
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dev.off()
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##### debug, grid 200x100
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nx <- 200
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ny <- 100
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alphamat <- matrix(1.1e-11, nrow = ny, ncol = nx)
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data.table::fwrite(alphamat, "debug_alpha.csv", col.names = FALSE)
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a <- read.table(
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textConnection(
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"H 1.11e+02 120.0,
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O 5.55e+01 55.1,
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Charge -2.0e-13 8.0e-17,
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C(-4) 2.0e-16 2.0e-15,
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C(4) 2.0e-03 0.2,
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Ca 2.0e-01 0.03,
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Cl 3.0e-01 0.5,
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Fe(2) 1.4e-04 0.0002,
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Fe(3) 1.3e-09 2.0e-08,
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H(0) 6.0e-12 2.0e-11,
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K 2.0e-03 1.0e-05,
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Mg 1.0e-02 0.2,
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Na 2.0e-01 0.3,
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S(-2) 5.9e-10 0,
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S(2) 8.3e-15 8.3e-12,
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S(4) 2.1e-14 5.1e-14,
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S(6) 1.6e-02 0.026,
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Sr 4.5e-04 0.045,
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U(4) 2.5e-09 2.5e-08,
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U(5) 1.6e-10 1.6e-10,
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U(6) 2.3e-07 1.0e-05"
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))
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vals <- t(a[, 2:3])
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nams <- c("H", "O", "Charge", "CH4", "C", "Ca", "Cl", "Fe2", "Fe3",
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"H0", "K", "Mg", "Na", "HS2", "S2", "S4", "S6","Sr", "U4",
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"U5", "U6")
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colnames(vals) <- nams
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rownames(vals) <- c("IC", "BC")
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vals
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length(nams)
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dim(vals)
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t(vals)
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ic <- matrix(rep(vals[1,], nx*ny), nrow = nx*ny, byrow = TRUE)
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colnames(ic) <- nams
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data.table::fwrite(ic, "debug_init.csv", col.names = TRUE)
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dput(vals[2,])
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out <- fread("debug_output.csv")
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x11()
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## cairo_pdf("debug_field_U6.pdf", width = 10, height = 6, family="serif")
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# out <- fread("./debug_output.csv")
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PlotField2(log10(out$U6), nx=nx, ny=ny, contour = FALSE, nlevels=10,
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palette = "cm.colors", plot.axes = FALSE, rev.palette = FALSE)
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##dev.off()
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## cairo_pdf("debug_field_Na.pdf", width = 10, height = 6, family="serif")
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out2 <- fread("./debug_output.csv")
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PlotField2(out2$Na, nx=nx, ny=ny, contour = FALSE, nlevels=10,
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palette = "topo.colors", plot.axes = FALSE, rev.palette = TRUE)
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## dev.off()
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out2$Na[seq(1, 200)]
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range(out2$Na)
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PlotField2(log10(out$U4), nx=nx, ny=ny, contour = FALSE, nlevels=10,
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palette = "terrain.colors", plot.axes = FALSE)
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out$U4[seq(50*200, 51*200)]
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PlotField2(out2$Fe3, nx=nx, ny=ny, contour = FALSE, nlevels=10,
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palette = "terrain.colors", plot.axes = FALSE)
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out2$Na[seq(20*200, 21*200)]
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out$Cl[seq(50*200, 51*200)]
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PlotField2(log10(out$Fe2), nx=nx, ny=ny, contour = FALSE, nlevels=12,
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palette = "terrain.colors", plot.axes = FALSE)
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PlotField2((out$Cl), nx=nx, ny=ny, contour = FALSE, nlevels=10,
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palette = "terrain.colors", plot.axes = FALSE)
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dev.off()
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library(Rcpp)
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cppFunction("static const std::vector<int> gen_seq(int from, int to) {
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int vsize = to - from + 1;
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std::vector<int> vec(vsize);
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for (int i = 0; i < vsize; i++) {
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vec[i] = i+from;
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}
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return vec;
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}")
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gen_seq(24, 49)
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cppFunction("static const std::vector<int> gen_vec(int elems) {
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std::vector<int> vec(elems);
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for (int i = 0; i < elems; i++) {
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vec[i] = i;
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}
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return vec;
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}")
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gen_vec(20)
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@ -41,14 +41,12 @@ static const std::vector<int> gen_vec(int elems) {
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return vec;
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}
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static const std::vector<int> gen_vec_rev(int from, int to) {
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int size = to - from+1;
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std::vector<int> vec(size);
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for (int i = from; i < to; i++) {
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vec[i] = i;
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std::cout << "i: " << i << "\n";
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static const std::vector<int> gen_seq(int from, int to) {
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int vsize = to - from + 1;
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std::vector<int> vec(vsize);
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for (int i = 0; i < vsize; i++) {
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vec[i] = i+from;
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}
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return vec;
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}
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@ -87,6 +85,7 @@ static bench_input barite_large_input = {
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.iterations = 5
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};
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static bench_input surfex_input = {
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.csv_file_init = "@SURFEX_BENCH@/surfex_init.csv",
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.csv_alpha_x = "@SURFEX_BENCH@/surfex_alpha.csv",
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@ -124,30 +123,41 @@ static bench_input surfex_input = {
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.iterations = 20
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};
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static bench_input debug_input = {
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.csv_file_init = "@SURFEX_BENCH@/surfex_init.csv",
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.csv_alpha_x = "@SURFEX_BENCH@/surfex_alpha.csv",
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.csv_alpha_y = "@SURFEX_BENCH@/surfex_alpha.csv",
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.ncols = 200,
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.nrows = 100,
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.s_x = 0.02,
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.s_y = 0.01,
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.boundary = {.north_const = gen_vec(100),
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.south_const = gen_seq(1, 19),
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.east_const = {},
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.west_const = gen_seq(50, 99),
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.values = {120.0, // H
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55.1, // O
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8.0e-17, // Charge
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2.0e-15, // CH4
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0.2, // C
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0.03, // Ca
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0.5, // Cl
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0.0002, // Fe2
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2.0e-08, // Fe3
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2.0e-11, // H0
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1.0e-05, // K
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0.2, // Mg
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0.3, // Na
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0, // HS2
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8.3e-12, // S2
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5.1e-14, // S4
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0.026, // S6
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0.045, // Sr
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2.5e-08, // U4
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1.6e-10, // U5
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1.0e-05}}, // U6
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.timestep = 86400,
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.iterations = 20
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};
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#endif // _BENCH_DEFS_HPP
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43
src/main.cpp
43
src/main.cpp
@ -23,29 +23,40 @@ int main(int argc, char **argv) {
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}
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if (with_output) {
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std::cout << "BARITE_200 started with output... ";
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timings[0] = run_bench(barite_200_input, "barite_200_output.csv");
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std::cout << "Runtime: " << timings[0] << " [ms]\n";
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// std::cout << "BARITE_200 started with output... ";
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// timings[0] = run_bench(barite_200_input, "barite_200_output.csv");
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// std::cout << "Runtime: " << timings[0] << " [ms]\n";
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std::cout << "BARITE_LARGE started with output... ";
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timings[1] = run_bench(barite_large_input, "barite_large_output.csv");
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std::cout << "Runtime: " << timings[1] << " [ms]\n";
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// std::cout << "BARITE_LARGE started with output... ";
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// timings[1] = run_bench(barite_large_input, "barite_large_output.csv");
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// std::cout << "Runtime: " << timings[1] << " [ms]\n";
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std::cout << "SURFEX started with output... ";
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timings[2] = run_bench(surfex_input, "surfex_output.csv");
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// std::cout << "SURFEX started with output... ";
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// timings[2] = run_bench(surfex_input, "surfex_output.csv");
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// std::cout << "Runtime: " << timings[2] << " [ms]\n";
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std::cout << "DEBUG started with output... ";
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timings[2] = run_bench(debug_input, "debug_output.csv");
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std::cout << "Runtime: " << timings[2] << " [ms]\n";
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} else {
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std::cout << "BARITE_200 started with no output... ";
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timings[0] = run_bench(barite_200_input);
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std::cout << " Runtime: " << timings[0] << " [ms]\n";
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std::cout << "BARITE_LARGE started with no output... ";
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timings[1] = run_bench(barite_large_input);
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std::cout << "Runtime: " << timings[1] << " [ms]\n";
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// std::cout << "BARITE_200 started with no output... ";
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// timings[0] = run_bench(barite_200_input);
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// std::cout << " Runtime: " << timings[0] << " [ms]\n";
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std::cout << "SURFEX started with no output... ";
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timings[2] = run_bench(surfex_input);
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// std::cout << "BARITE_LARGE started with no output... ";
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// timings[1] = run_bench(barite_large_input);
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// std::cout << "Runtime: " << timings[1] << " [ms]\n";
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// std::cout << "SURFEX started with no output... ";
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// timings[2] = run_bench(surfex_input);
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// std::cout << "Runtime: " << timings[2] << " [ms]\n";
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std::cout << "DEBUG started with no output... ";
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timings[2] = run_bench(debug_input);
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std::cout << "Runtime: " << timings[2] << " [ms]\n";
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}
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return EXIT_SUCCESS;
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