crone: Structural Crystallography in 1d

# 
# This file is part of the crone package
#


# Use this function only once. It returns a list with
# dataframes as elements. Each dataframe corresponds to
# anomalous data for a specific chamical element. The
# list name is anomalous_data. After having used this
# function, and while still in the R workspace, type:
# 
#   save(anomalous_data,file="data/anomalous_data.RData")
#


  
create_anom_dataframe <- function()
{
  # Vector with atom names
  anames <- c("H","He","Li","Be","B","C","N","O","F","Ne",
              "Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca",
              "Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Xe")
  
  anomalous_data <- list()
  for (chem_el in anames)
  {
   # Load specific dataset of f' and f"
   filename <- file.path("data-raw",paste(chem_el,".dat",sep=""))
   ad <- read.table(file=filename)
  
   # Turn energies (in ev) into wavelength (in angstroms)
   ad$V1 <- 12400/ad$V1
  
   # Reverse order (because of inverse relation between energy 
   # and wavelength)
   ad <- ad[order(ad[,1]),]
  
   # Appropriate names
   colnames(ad) <- c("lambda","f1","f2")
   
   anomalous_data <- c(anomalous_data,list(ad))
  }
  names(anomalous_data) <- anames
  
  return(anomalous_data)
}

# Use this function from within main Package directory to generate
# data file "atoms.RData" in data/

generate_atoms_dataframe <- function()
{
  # Vector with atom names
  anames <- c(" H","He","Li","Be"," B"," C"," N"," O"," F","Ne",
              "Na","Mg","Al","Si"," P"," S","Cl","Ar"," K","Ca",
              "Sc","Ti"," V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Xe")

  # Vector with atom numbers (Z)
  anumbers <- c(1:30,54)

  # Dataframe including atom names and numbers
  atoms <- data.frame(anames=I(anames),Z=anumbers)
  
  # Save as file Rda
  save(atoms,file="data/atoms.RData")
}

# Use this function to generate ksigma and anoK objects
# as internal data (in R/sysdata.rda)
generate_global_vars <- function()
{
  require(devtools)
  
  # k constant determining gaussian sigma
  ksigma <- 0.05
  
  # anoK to soften anomalous scattering effect
  anoK <- 0.3
  
  # Save all data
  use_data(ksigma,anoK,internal=TRUE)
}

# Use the following function only once to create all "*_h.dat" data files
# under inst/extdata. The function has to be sourced from an RStudio
# session in directory "crone". The files produced will be 
# automatically copied in inst/extdata/.
generate_h_data <- function() {
  # beryllium_fluoride
  sdata <- load_structure("beryllium_fluoride")
  hidx <- 1:10
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9195)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/beryllium_fluoride",fdata)
  
  # carbon_dioxide
  sdata <- load_structure("carbon_dioxide")
  hidx <- 1:10
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9196)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/carbon_dioxide",fdata)
  
  # cyanate
  sdata <- load_structure("cyanate")
  hidx <- 1:10
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9197)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/cyanate",fdata)
  
  # nitronium
  sdata <- load_structure("nitronium")
  hidx <- 1:20
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.01
  set.seed(9198)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/nitronium",fdata)
  
  # thiocyanate
  sdata <- load_structure("thiocyanate")
  hidx <- 1:10
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9199)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/thiocyanate",fdata)
  
  # xenon_difluoride
  sdata <- load_structure("xenon_difluoride")
  hidx <- 1:20
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9200)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/xenon_difluoride",fdata)
  
  # pinkerton2015
  sdata <- load_structure("pinkerton2015")
  hidx <- 1:12
  ftmp <- strufac(hidx,sdata)
  vx0err <- 0.15
  set.seed(9200)
  ftmp2 <- sfobs(hidx,sdata,vx0err)
  fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,
                             Fobs=ftmp2$F,sigFobs=ftmp2$sF,
                             Phicalc=ftmp$Fpha)
  write_h("inst/extdata/pinkerton2015",fdata)
}