Compare `03e573f ... +4 ... 6909863`

#' \code{\link{plot.default}}. See details for further information
#'
#' @return This function returns an RLum.Results object from the illumination simulation.
#' 
#'
#' @section Function version: 0.1.1
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),

@@ -41,8 +41,7 @@

){

# check input arguments ---------------------------------------------------

  ##check if temperature is > 0 K (-273 degree celsius)
  ##check if temperature is > 0 K (-273 degree Celsius)
  if(temp < -273){
    stop("\n [.simulate_illumination()] Argument 'temp' has to be > 0 K!")
  }

@@ -72,7 +71,6 @@

72	71		# P: Photonflux (in Bailey 2002/2004: wavelength [nm]) = 1
73	72		# b: heating rate [deg. C/s] = 0
74	73		##============================================================================##
75		-
76	74		if(parms$model == "Bailey2004" \|\| parms$model == "Bailey2002"){
77	75		P <- 0.02/(1.610^(-19)(1240/470))*(optical_power/100)
78	76		}

@@ -96,7 +94,7 @@

96	94		times = times,
97	95		parms = parms))
98	96		##============================================================================##
99		-	# SOLVING ODE (deSolve requiered)
	97	+	# SOLVING ODE (deSolve required)
100	98		##============================================================================##
101	99		out <- deSolve::ode(y = n, times = times, parms = parameters.step, func = .set_ODE_Rcpp, rtol=1e-3, atol=1e-3, maxsteps=1e5, method = "bdf")
102	100		##============================================================================##

@@ -12,7 +12,7 @@

#' \bold{A}: conduction band to electron/hole trap transition probability in s^(-1)
#' \bold{B}: valence band to hole trap transition probability in s^(-1)
#' \bold{Th}: photo-ionisation cross-section in s^(-1)
#' \bold{E_th}: `thermal assistance' energy in eV
#' \bold{E_th}: thermal assistance energy in (eV)
#' \bold{n}: concentrations of electron/hole traps after sample history in cm^(-3)
#'
#' @note \bold{n} are the saved concentrations of the last step of the sample history

@@ -106,6 +106,39 @@

106	106		# dimensionless constant (for Details see Wintle (1975))
107	107		K <- 2.8e7
108	108
	109	+	## add parameter names
	110	+	names <- c(
	111	+	N = "concentration of electron traps",
	112	+	E = "depth below conduction or valence band",
	113	+	s = "frequency factor",
	114	+	A = "transiation probability to conduction or valence band",
	115	+	B = "conduction band to hole centre transition probability",
	116	+	Th = "photo-ionisation cross-section ",
	117	+	E_th = "thermal assistance energy",
	118	+	n = "concentration of trapped charges",
	119	+	k_B = "Boltzmann constant",
	120	+	W = "activation energy",
	121	+	K = "dimensionlss constant after Wintle (1975)")
	122	+
	123	+	## add units
	124	+	units <- c(
	125	+	N = "cm^-3",
	126	+	E = "eV",
	127	+	s = "s^-1",
	128	+	A = "cm^3 s^-1",
	129	+	B = "cm^3 s^-1",
	130	+	Th = "s^-1",
	131	+	E_th = "eV",
	132	+	n = "cm^-3",
	133	+	k_B = "eV K^-1",
	134	+	W = "eV",
	135	+	K = "")
	136	+
	137	+	## to enter a new model, the structure is as follows:
	138	+	## First numbers all related to electron traps if B = 0
	139	+	## Followed by parameters for the recombination centres
	140	+	## Th and E_th refer to traps only
	141	+	## n: first traps, then recombination centres, then n_c then n_v
109	142		parameter.list = list(
110	143		Bailey2001 = list(
111	144		N = c(1.5e7, 1e7, 1e9, 2.5e8, 5e10, 3e8, 1e10, 5e9, 1e11),

@@ -122,6 +155,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
      ),


@@ -141,6 +176,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    ),


@@ -160,6 +197,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    ),


@@ -178,6 +217,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    ),


@@ -197,6 +238,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    ),


@@ -215,6 +258,8 @@

      k_B = k_B,
      K = K,
      W = W,
      units  = units,
      names = names,
      model = model
    ),


@@ -233,6 +278,8 @@

      k_B = k_B,
      K = K,
      W = W,
      units  = units,
      names = names,
      model = model
    ),


@@ -242,6 +289,8 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    ),


@@ -251,10 +300,13 @@

      k_B = k_B,
      W = W,
      K = K,
      units  = units,
      names = names,
      model = model
    )
  )


  switch(model,
        "Bailey2001" = {
          return(parameter.list$Bailey2001)

@@ -581,16 +581,13 @@

        start_temp <- ifelse(is.null(own_start_temperature), 20, own_start_temperature)

        if(!is.null(own_state_parameters)){ ## state parameters submitted

          own_state_parameters <- c(own_state_parameters, 0, 0)

          n <- Luminescence::set_RLum(class = "RLum.Results",
                                      data = list(n = own_state_parameters,
                                                  temp = start_temp,
                                                  model = model))

        } else { ## no state parameters submitted

          n <- Luminescence::set_RLum(class = "RLum.Results",
                                      data = list(n = rep(0,length(parms$N)+2),
                                                  temp = start_temp,

@@ -636,9 +633,7 @@

636	633
637	634
638	635		# Plot settings -------------------------------------------------------------------------------
639		-
640	636		if(plot){
641		-
642	637		plot.data <- get_RLum(model.output,
643	638		recordType = c("RF$", "TL$", "OSL$", "LM-OSL$", "RF_heating$", "pause$"),
644	639		drop = FALSE)

@@ -1,7 +1,7 @@

//set_ODE_Rcpp.cpp
//author: Johannes Friedrich, University of Bayreuth (Germany)
//version: 0.1.1 [2016-04-04]
//Function calculates the ODEs for all quartz luminescence models iterativly
//Function calculates the ODEs for all quartz luminescence models iteratively
//



@@ -13,7 +13,6 @@

List set_ODE_Rcpp(double t, arma::vec n, Rcpp::List parameters) {

  //unpack parameters for ODEs

  arma::vec N = parameters["N"];
  arma::vec E = parameters["E"];
  arma::vec s = parameters["s"];

@@ -34,7 +33,7 @@

 int j = 0;
 int jj = 0;
 for (std::size_t i = 0; i < N.size(); ++i){
   if (B[i] == 0)    {//use recombination propability of recombination centers to identify electron traps, because they had no recombination propability to recomibnation centers from conduction band
   if (B[i] == 0)    {//use recombination probability of recombination centers to identify electron traps, because they had no recombination probability to recombination centers from conduction band
     j++;
     jj++;


@@ -46,7 +45,6 @@

 }

  //build sub-vectors for conduction/valence band calculation
  
  arma::vec temp_dn1 = dn.subvec(0,j-1);
  arma::vec temp_dn2 = dn.subvec(j,jj-1);


@@ -60,7 +60,7 @@

  ##### check temperature differences between different steps ####

  #check if temperatures of step before is lower than current sequence step and if step is not PH or CH
  #automatically heat to temperatrue of current sequence step
  #automatically heat to temperature of current sequence step

  #check if "temp" or "temp_begin" (only for TL) is part of the sequence, if not, the first entry in sequence is temp (per definition)
  if(!"temp" %in% names(sequence[[i]]) && !"temp_begin" %in% names(sequence[[i]])) {names(sequence[[i]])[1] <- "temp"}

@@ -69,7 +69,7 @@

  if("temp_begin" %in% names(sequence[[i]])) {sequence[[i]]["temp"] <- sequence[[i]]["temp_begin"]}

  #check if temperature is higher than the step before
  #automatically heat to temperatrue of current sequence step, except stepname is "PH" or "CH"
  #automatically heat to temperature of current sequence step, except stepname is "PH" or "CH"
  if(((n$temp < sequence[[i]]["temp"])&&(names(sequence)[i] != "PH")&&(names(sequence)[i] != "CH")) == TRUE){
    n <- .simulate_heating(temp_begin = n$temp,temp_end = sequence[[i]]["temp"], heating_rate = 1, n, parms)


@@ -362,7 +362,7 @@


    output.model <- c(output.model, n$RF_heating.data, n$concentrations)

    ##pause to releax
    ##pause to relax
    n <- .simulate_pause(temp = sequence[[i]]["temp_end"], duration = 5, n = n, parms = parms)

    ##collect originators

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6909863

Hiding 4 contexual commits

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03e573f

Files		•	•	•	Coverage
Project Totals (20 files)	1,189	1,098	0	91	92.35%

178	217		k_B = k_B,
179	218		W = W,
180	219		K = K,
	220	+	units = units,
	221	+	names = names,
181	222		model = model
182	223		),
183	224

215	258		k_B = k_B,
216	259		K = K,
217	260		W = W,
	261	+	units = units,
	262	+	names = names,
218	263		model = model
219	264		),
220	265

233	278		k_B = k_B,
234	279		K = K,
235	280		W = W,
	281	+	units = units,
	282	+	names = names,
236	283		model = model
237	284		),
238	285

242	289		k_B = k_B,
243	290		W = W,
244	291		K = K,
	292	+	units = units,
	293	+	names = names,
245	294		model = model
246	295		),
247	296

251	300		k_B = k_B,
252	301		W = W,
253	302		K = K,
	303	+	units = units,
	304	+	names = names,
254	305		model = model
255	306		)
256	307		)
257	308
	309	+
258	310		switch(model,
259	311		"Bailey2001" = {
260	312		return(parameter.list$Bailey2001)

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6 Commits

17	17		#' \code{\link{plot.default}}. See details for further information
18	18		#'
19	19		#' @return This function returns an RLum.Results object from the illumination simulation.
20		-	#'
	20	+	#'
21	21		#' @section Function version: 0.1.1
22	22		#'
23	23		#' @author Johannes Friedrich, University of Bayreuth (Germany),

41	41		){
42	42
43	43		# check input arguments ---------------------------------------------------
44		-
45		-	##check if temperature is > 0 K (-273 degree celsius)
	44	+	##check if temperature is > 0 K (-273 degree Celsius)
46	45		if(temp < -273){
47	46		stop("\n [.simulate_illumination()] Argument 'temp' has to be > 0 K!")
48	47		}

12	12		#' \bold{A}: conduction band to electron/hole trap transition probability in s^(-1)
13	13		#' \bold{B}: valence band to hole trap transition probability in s^(-1)
14	14		#' \bold{Th}: photo-ionisation cross-section in s^(-1)
15		-	#' \bold{E_th}: `thermal assistance' energy in eV
	15	+	#' \bold{E_th}: thermal assistance energy in (eV)
16	16		#' \bold{n}: concentrations of electron/hole traps after sample history in cm^(-3)
17	17		#'
18	18		#' @note \bold{n} are the saved concentrations of the last step of the sample history

581	581		start_temp <- ifelse(is.null(own_start_temperature), 20, own_start_temperature)
582	582
583	583		if(!is.null(own_state_parameters)){ ## state parameters submitted
584		-
585	584		own_state_parameters <- c(own_state_parameters, 0, 0)
586		-
587	585		n <- Luminescence::set_RLum(class = "RLum.Results",
588	586		data = list(n = own_state_parameters,
589	587		temp = start_temp,
590	588		model = model))
591	589
592	590		} else { ## no state parameters submitted
593		-
594	591		n <- Luminescence::set_RLum(class = "RLum.Results",
595	592		data = list(n = rep(0,length(parms$N)+2),
596	593		temp = start_temp,

1	1		//set_ODE_Rcpp.cpp
2	2		//author: Johannes Friedrich, University of Bayreuth (Germany)
3	3		//version: 0.1.1 [2016-04-04]
4		-	//Function calculates the ODEs for all quartz luminescence models iterativly
	4	+	//Function calculates the ODEs for all quartz luminescence models iteratively
5	5		//
6	6
7	7

13	13		List set_ODE_Rcpp(double t, arma::vec n, Rcpp::List parameters) {
14	14
15	15		//unpack parameters for ODEs
16		-
17	16		arma::vec N = parameters["N"];
18	17		arma::vec E = parameters["E"];
19	18		arma::vec s = parameters["s"];

34	33		int j = 0;
35	34		int jj = 0;
36	35		for (std::size_t i = 0; i < N.size(); ++i){
37		-	if (B[i] == 0) {//use recombination propability of recombination centers to identify electron traps, because they had no recombination propability to recomibnation centers from conduction band
	36	+	if (B[i] == 0) {//use recombination probability of recombination centers to identify electron traps, because they had no recombination probability to recombination centers from conduction band
38	37		j++;
39	38		jj++;
40	39

46	45		}
47	46
48	47		//build sub-vectors for conduction/valence band calculation
49		-
50	48		arma::vec temp_dn1 = dn.subvec(0,j-1);
51	49		arma::vec temp_dn2 = dn.subvec(j,jj-1);
52	50

60	60		##### check temperature differences between different steps ####
61	61
62	62		#check if temperatures of step before is lower than current sequence step and if step is not PH or CH
63		-	#automatically heat to temperatrue of current sequence step
	63	+	#automatically heat to temperature of current sequence step
64	64
65	65		#check if "temp" or "temp_begin" (only for TL) is part of the sequence, if not, the first entry in sequence is temp (per definition)
66	66		if(!"temp" %in% names(sequence[[i]]) && !"temp_begin" %in% names(sequence[[i]])) {names(sequence[[i]])[1] <- "temp"}

69	69		if("temp_begin" %in% names(sequence[[i]])) {sequence[[i]]["temp"] <- sequence[[i]]["temp_begin"]}
70	70
71	71		#check if temperature is higher than the step before
72		-	#automatically heat to temperatrue of current sequence step, except stepname is "PH" or "CH"
	72	+	#automatically heat to temperature of current sequence step, except stepname is "PH" or "CH"
73	73		if(((n$temp < sequence[[i]]["temp"])&&(names(sequence)[i] != "PH")&&(names(sequence)[i] != "CH")) == TRUE){
74	74		n <- .simulate_heating(temp_begin = n$temp,temp_end = sequence[[i]]["temp"], heating_rate = 1, n, parms)
75	75

160	197		k_B = k_B,
161	198		W = W,
162	199		K = K,
	200	+	units = units,
	201	+	names = names,
163	202		model = model
164	203		),
165	204

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362	362
363	363		output.model <- c(output.model, n$RF_heating.data, n$concentrations)
364	364
365		-	##pause to releax
	365	+	##pause to relax
366	366		n <- .simulate_pause(temp = sequence[[i]]["temp_end"], duration = 5, n = n, parms = parms)
367	367
368	368		##collect originators

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