R: Model Luminescence Signals

model_LuminescenceSignals {RLumModel}

R Documentation

Model Luminescence Signals

Description

This function models luminescence signals for quartz based on published physical models. It is possible to simulate TL, (CW-) OSL, RF measurements in a arbitrary sequence. This sequence is defined as a list of certain aberrations. Furthermore it is possible to load a sequence direct from the Risø Sequence Editor. The output is an Luminescence::RLum.Analysis object and so the plots are done by the Luminescence::plot_RLum.Analysis function. If a SAR sequence is simulated the plot output can be disabled and SAR analyse functions can be used.

Usage

model_LuminescenceSignals(
  model,
  sequence,
  lab.dose_rate = 1,
  simulate_sample_history = FALSE,
  plot = TRUE,
  verbose = TRUE,
  show_structure = FALSE,
  own_parameters = NULL,
  own_state_parameters = NULL,
  own_start_temperature = NULL,
  ...
)

Arguments

`model`	character (required): set model to be used. Available models are: `"Bailey2001"`, `"Bailey2002"`, `"Bailey2004"`, `"Pagonis2007"`, `"Pagonis2008"`, `"Friedrich2017"`, `"Friedrich2018"`, `⁠"Peng2022⁠`" and for own models `"customized"` (or `"customised"`). Note: When model = `"customized"`/`⁠"customised⁠` is set, the argument `own_parameters` has to be set.
`sequence`	list (required): set sequence to model as list or as *.seq file from the Risø sequence editor. To simulate SAR measurements there is an extra option to set the sequence list (cf. details).
`lab.dose_rate`	numeric (with default): laboratory dose rate in XXX Gy/s for calculating seconds into Gray in the *.seq file.
`simulate_sample_history`	logical (with default): `FALSE` (with default): simulation begins at laboratory conditions, `TRUE`: simulations begins at crystallization process (all levels 0)
`plot`	logical (with default): Enables or disables plot output
`verbose`	logical (with default): Verbose mode on/off
`show_structure`	logical (with default): Shows the structure of the result. Recommended to show `record.id` to analyse concentrations.
`own_parameters`	list (with default): This argument allows the user to submit own parameter sets. See details for more information.
`own_state_parameters`	numeric (with default): Some publications (e.g., Pagonis 2009) offer state parameters. With this argument the user can submit this state parameters. For further details see vignette "RLumModel - Using own parameter sets" and example 3. The parameter also accepts an Luminescence::RLum.Results object created by .set_pars as input.
`own_start_temperature`	numeric (with default): Parameter to control the start temperature (in ºC) of a simulation. This parameter takes effect only when 'model = "customized"' is chosen.
`...`	further arguments and graphical parameters passed to plot.default. See details for further information.

Details

Defining a sequence

Arguments	Description	Sub-arguments
`TL`	thermally stimulated luminescence	'temp begin' (ºC), 'temp end' (ºC), 'heating rate' (ºC/s)
`OSL`	optically stimulated luminescence	'temp' (ºC), 'duration' (s), 'optical_power' (%)
`ILL`	illumination	'temp' (ºC), 'duration' (s), 'optical_power' (%)
`LM_OSL`	linear modulated OSL	'temp' (ºC), 'duration' (s), optional: 'start_power' (%), 'end_power' (%)
`RL/RF`	radioluminescence	'temp' (ºC), 'dose' (Gy), 'dose_rate' (Gy/s)
`RF_heating`	RF during heating/cooling	'temp begin' (ºC), 'temp end' (ºC), 'heating rate' (ºC/s], 'dose_rate' (Gy/s)
`IRR`	irradiation	'temp' (ºC), 'dose' (Gy), 'dose_rate' (Gy/s)
`CH`	cutheat	'temp' (ºC), optional: 'duration' (s), 'heating_rate' (ºC/s)
`PH`	preheat	'temp' (ºC), 'duration' (s), optional: 'heating_rate' (ºC/s)
`PAUSE`	pause	'temp' (ºC), 'duration' (s)

Note: 100% illumination power equates to 20 mW/cm^2

Own parameters

The list has to contain the following items:

N: Concentration of electron- and hole traps (cm^(-3))
E: Electron/Hole trap depth (eV)
s: Frequency factor (s^(-1))
A: Conduction band to electron trap and valence band to hole trap transition probability (s^(-1) * cm^(3)). CAUTION: Not every publication uses the same definition of parameter A and B! See vignette "RLumModel - Usage with own parameter sets" for further details
B: Conduction band to hole centre transition probability (s^(-1) * cm^(3)).
Th: Photo-eviction constant or photoionisation cross section, respectively
E_th: Thermal assistence energy (eV)
k_B: Boltzman constant 8.617e-05 (eV/K)
W: activation energy 0.64 (eV) (for UV)
K: 2.8e7 (dimensionless constant)
model: "customized"
R (optional): Ionisation rate (pair production rate) equivalent to 1 Gy/s (s^(-1)) * cm^(-3))

For further details see Bailey 2001, Wintle 1975, vignette "RLumModel - Using own parameter sets" and example 3.

Defining a SAR-sequence

Abrivation	Description	examples
`RegDose`	Dose points of the regenerative cycles (Gy)	c(0, 80, 140, 260, 320, 0, 80)
`TestDose`	Test dose for the SAR cycles (Gy)	50
`PH`	Temperature of the preheat (ºC)	240
`CH`	Temperature of the cutheat (ºC)	200
`OSL_temp`	Temperature of OSL read out (ºC)	125
`OSL_duration`	Duration of OSL read out (s)	default: 40
`Irr_temp`	Temperature of irradiation (ºC)	default: 20
`PH_duration`	Duration of the preheat (s)	default: 10
`dose_rate`	Dose rate of the laboratory irradiation source (Gy/s)	default: 1
`optical_power`	Percentage of the full illumination power (%)	default: 90
`Irr_2recover`	Dose to be recovered in a dose-recovery-test (Gy)	20

Value

This function returns an Luminescence::RLum.Analysis object with all TL, (LM-) OSL and RF/RL steps in the sequence. Every entry is an Luminescence::RLum.Data.Curve object and can be plotted, analysed etc. with further RLum-functions.

Function version

0.1.6

How to cite

Friedrich, J., Kreutzer, S., 2022. model_LuminescenceSignals(): Model Luminescence Signals. Function version 0.1.6. In: Friedrich, J., Kreutzer, S., Schmidt, C., 2022. RLumModel: Solving Ordinary Differential Equations to Understand Luminescence. R package version 0.2.10. https://CRAN.R-project.org/package=RLumModel

Author(s)

Johannes Friedrich, University of Bayreuth (Germany), Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University (United Kingdom)

References

Bailey, R.M., 2001. Towards a general kinetic model for optically and thermally stimulated luminescence of quartz. Radiation Measurements 33, 17-45.

Bailey, R.M., 2002. Simulations of variability in the luminescence characteristics of natural quartz and its implications for estimates of absorbed dose. Radiation Protection Dosimetry 100, 33-38.

Bailey, R.M., 2004. Paper I-simulation of dose absorption in quartz over geological timescales and it simplications for the precision and accuracy of optical dating. Radiation Measurements 38, 299-310.

Friedrich, J., Kreutzer, S., Schmidt, C., 2016. Solving ordinary differential equations to understand luminescence: 'RLumModel', an advanced research tool for simulating luminescence in quartz using R. Quaternary Geochronology 35, 88-100.

Friedrich, J., Pagonis, V., Chen, R., Kreutzer, S., Schmidt, C., 2017: Quartz radiofluorescence: a modelling approach. Journal of Luminescence 186, 318-325.

Pagonis, V., Chen, R., Wintle, A.G., 2007: Modelling thermal transfer in optically stimulated luminescence of quartz. Journal of Physics D: Applied Physics 40, 998-1006.

Pagonis, V., Wintle, A.G., Chen, R., Wang, X.L., 2008. A theoretical model for a new dating protocol for quartz based on thermally transferred OSL (TT-OSL). Radiation Measurements 43, 704-708.

Pagonis, V., Lawless, J., Chen, R., Anderson, C., 2009. Radioluminescence in Al2O3:C - analytical and numerical simulation results. Journal of Physics D: Applied Physics 42, 175107 (9pp).

Peng, J., Wang, X., Adamiec, G., 2022. The build-up of the laboratory-generated dose-response curve and underestimation of equivalent dose for quartz OSL in the high dose region: A critical modelling study. Quaternary Geochronology 67, 101231.

Soetaert, K., Cash, J., Mazzia, F., 2012. Solving differential equations in R. Springer Science & Business Media.

Wintle, A., 1975. Thermal Quenching of Thermoluminescence in Quartz. Geophysical Journal International 41, 107-113.

Examples


##================================================================##
## 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"
   )


## End(Not run)

[Package RLumModel version 0.2.10 Index]