# NOT RUN {
##================================================================##
## Example 1: Simulate Bailey2001
## (cf. Bailey, 2001, Fig. 1)
##================================================================##
##set sequence with the following steps
## (1) Irradiation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
## (2) TL from 20-400 deg. C with a rate of 5 K/s
sequence <-
list(
IRR = c(20, 10, 1),
TL = c(20, 400, 5)
)
##model sequence
model.output <- model_LuminescenceSignals(
sequence = sequence,
model = "Bailey2001"
)
##get all TL concentrations
TL_conc <- get_RLum(model.output, recordType = "(TL)", drop = FALSE)
plot_RLum(TL_conc)
##plot 110 deg. C trap concentration
TL_110 <- get_RLum(TL_conc, recordType = "conc. level 1")
plot_RLum(TL_110)
##============================================================================##
## Example 2: compare different optical powers of stimulation light
##============================================================================##
# call function "model_LuminescenceSignals", model = "Bailey2004"
# and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence
# the optical_power of the LED is varied and then compared.
optical_power <- seq(from = 0,to = 100,by = 20)
model.output <- lapply(optical_power, function(x){
sequence <- list(IRR = c(20, 50, 1),
PH = c(220, 10, 5),
OSL = c(125, 50, x)
)
data <- model_LuminescenceSignals(
sequence = sequence,
model = "Bailey2004",
plot = FALSE,
verbose = FALSE
)
return(get_RLum(data, recordType = "OSL$", drop = FALSE))
})
##combine output curves
model.output.merged <- merge_RLum(model.output)
##plot
plot_RLum(
object = model.output.merged,
xlab = "Illumination time [s]",
ylab = "OSL signal [a.u.]",
main = "OSL signal dependency on optical power of stimulation light",
legend.text = paste("Optical power density", 20*optical_power/100, "mW/cm^2"),
combine = TRUE)
##============================================================================##
## Example 3: Usage of own parameter sets (Pagonis 2009)
##============================================================================##
own_parameters <- list(
N = c(2e15, 2e15, 1e17, 2.4e16),
E = c(0, 0, 0, 0),
s = c(0, 0, 0, 0),
A = c(2e-8, 2e-9, 4e-9, 1e-8),
B = c(0, 0, 5e-11, 4e-8),
Th = c(0, 0),
E_th = c(0, 0),
k_B = 8.617e-5,
W = 0.64,
K = 2.8e7,
model = "customized",
R = 1.7e15
)
## Note: In Pagonis 2009 is B the valence band to hole centre probability,
## but in Bailey 2001 this is A_j. So the values of B (in Pagonis 2009)
## are A in the notation above. Also notice that the first two entries in N, A and
## B belong to the electron traps and the last two entries to the hole centres.
own_state_parameters <- c(0, 0, 0, 9.4e15)
## calculate Fig. 3 in Pagonis 2009. Note: The labels for the dose rate in the original
## publication are not correct.
## For a dose rate of 0.1 Gy/s belongs a RF signal to ~ 1.5e14 (see Fig. 6).
sequence <- list(RF = c(20, 0.1, 0.1))
model_LuminescenceSignals(
model = "customized",
sequence = sequence,
own_parameters = own_parameters,
own_state_parameters = own_state_parameters)
# }
# NOT RUN {
##============================================================================##
## Example 4: Simulate Thermal-Activation-Characteristics (TAC)
##============================================================================##
##set temperature
act.temp <- seq(from = 80, to = 600, by = 20)
##loop over temperature
model.output <- vapply(X = act.temp, FUN = function(x) {
##set sequence, note: sequence includes sample history
sequence <- list(
IRR = c(20, 1, 1e-11),
IRR = c(20, 10, 1),
PH = c(x, 1),
IRR = c(20, 0.1, 1),
TL = c(20, 150, 5)
)
##run simulation
temp <- model_LuminescenceSignals(
sequence = sequence,
model = "Pagonis2007",
simulate_sample_history = TRUE,
plot = FALSE,
verbose = FALSE
)
## "TL$" for exact matching TL and not (TL)
TL_curve <- get_RLum(temp, recordType = "TL$")
##return max value in TL curve
return(max(get_RLum(TL_curve)[,2]))
}, FUN.VALUE = 1)
##plot resutls
plot(
act.temp[-(1:3)],
model.output[-(1:3)],
type = "b",
xlab = "Temperature [\u00B0C]",
ylab = "TL [a.u.]"
)
##============================================================================##
## Example 5: Simulate SAR sequence
##============================================================================##
##set SAR sequence with the following steps
## (1) RegDose: set regenerative dose [Gy] as vector
## (2) TestDose: set test dose [Gy]
## (3) PH: set preheat temperature in deg. C
## (4) CH: Set cutheat temperature in deg. C
## (5) OSL_temp: set OSL reading temperature in deg. C
## (6) OSL_duration: set OSL reading duration in s
sequence <- list(
RegDose = c(0,10,20,50,90,0,10),
TestDose = 5,
PH = 240,
CH = 200,
OSL_temp = 125,
OSL_duration = 70)
# call function "model_LuminescenceSignals", set sequence = sequence,
# model = "Pagonis2007" (palaeodose = 20 Gy) and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence
model.output <- model_LuminescenceSignals(
sequence = sequence,
model = "Pagonis2007",
plot = FALSE
)
# in environment is a new object "model.output" with the results of
# every step of the given sequence.
# Plots are done at OSL and TL steps and the growth curve
# call "analyse_SAR.CWOSL" from RLum package
results <- analyse_SAR.CWOSL(model.output,
signal.integral.min = 1,
signal.integral.max = 15,
background.integral.min = 601,
background.integral.max = 701,
fit.method = "EXP",
dose.points = c(0,10,20,50,90,0,10))
##============================================================================##
## Example 6: generate sequence from *.seq file and run SAR simulation
##============================================================================##
# load example *.SEQ file and construct a sequence.
# call function "model_LuminescenceSignals", load created sequence for sequence,
# set model = "Bailey2002" (palaeodose = 10 Gy)
# and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence
path <- system.file("extdata", "example_SAR_cycle.SEQ", package="RLumModel")
sequence <- read_SEQ2R(file = path)
model.output <- model_LuminescenceSignals(
sequence = sequence,
model = "Bailey2001",
plot = FALSE
)
## call RLum package function "analyse_SAR.CWOSL" to analyse the simulated SAR cycle
results <- analyse_SAR.CWOSL(model.output,
signal.integral.min = 1,
signal.integral.max = 10,
background.integral.min = 301,
background.integral.max = 401,
dose.points = c(0,8,14,26,32,0,8),
fit.method = "EXP")
print(get_RLum(results))
##============================================================================##
## Example 7: Simulate sequence at laboratory without sample history
##============================================================================##
##set sequence with the following steps
## (1) Irraditation at 20 deg. C with a dose of 100 Gy and a dose rate of 1 Gy/s
## (2) Preheat to 200 deg. C and hold for 10 s
## (3) LM-OSL at 125 deg. C. for 100 s
## (4) Cutheat at 200 dec. C.
## (5) Irraditation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
## (6) Pause at 200 de. C. for 100 s
## (7) OSL at 125 deg. C for 100 s with 90 % optical power
## (8) Pause at 200 deg. C for 100 s
## (9) TL from 20-400 deg. C with a heat rate of 5 K/s
## (10) Radiofluorescence at 20 deg. C with a dose of 200 Gy and a dose rate of 0.01 Gy/s
sequence <-
list(
IRR = c(20, 100, 1),
PH = c(200, 10),
LM_OSL = c(125, 100),
CH = c(200),
IRR = c(20, 10, 1),
PAUSE = c(200, 100),
OSL = c(125, 100, 90),
PAUSE = c(200, 100),
TL = c(20, 400, 5),
RF = c(20, 200, 0.01)
)
# call function "model_LuminescenceSignals", set sequence = sequence,
# model = "Pagonis2008" (palaeodose = 200 Gy) and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence
model.output <- model_LuminescenceSignals(
sequence = sequence,
model = "Pagonis2008"
)
# }
Run the code above in your browser using DataCamp Workspace