public JComplex generateF0(JVector Q, int Z, JComplex energyFormFactor) {
JComplex f0 = new JComplex(0, 0);
double fTemp = elementConstants[Z - 1][9];
for (int i = 1; i < 5; i++) {
double ai = elementConstants[Z - 1][i];
double bi = elementConstants[Z - 1][i + 4];
fTemp += ai * Math.exp(-1 * bi * Math.pow((Q.length()) / (4 * Math.PI), 2));
}
f0 = JComplex.add(energyFormFactor, fTemp);
return f0;
}
/**
* This method searches through the "sf" folder which contains the complex scattering factors at a
* number of energies in eV for the desired energy. These files were obtained from the Berkeley
* National Lab. url http://henke.lbl.gov/optical_constants/asf.html The files that will be
* searched only have energy values between 10eV and 30keV. If a selection of > 30keV is made then
* a complex value of Z + 0*i will be returned.
*
* @param energyOrWavelength set to 0 for an Energy in eV input. set to 1 for a wavelength in
* Angstroms input
* @param findMe The energy or wavelength that is to be found in the list
* @param Z The number of electrons in the element
* @return The complex scattering factor for the desired energy or wavelength
* @throws Exception If the energyOrWavelength toggle is < 0 or > 1 then an exception is thrown.
* If Z < 0 or > 92 an exception is thrown. If E < 10 eV or lambda > 1238.174 Angstroms an
* exception is thrown
*/
public JComplex getComplexF(int energyOrWavelength, double findMe, int Z) throws Exception {
/* make sure the input is 0 or 1 */
if (energyOrWavelength < 0 || energyOrWavelength > 1)
throw new Exception(
"Your selection of "
+ energyOrWavelength
+ " does not fall within the constraints."
+ "\nIf you want energy, set the energyOrWavelength value to 0.\nIf you want wavelength, set the energyOrWavelength value to 1.");
/* make sure the 0 < Z < 92 */
if (Z < 0 || Z > 92)
throw new Exception(
"Your selection of "
+ Z
+ " does not fall within the current number of elements. Please choose a Z such that 0 < Z < 92");
/* Declare the file reader */
FileReader fr = null;
/* define Planck's constant in terms of eV*s */
double h = 4.13566733e-15;
/* define the speed of light in terms of Angstroms / second */
double c = 2.99792458e18;
/* If the user passes in a wavelength (energyOrWavelength == 1), convert the wavelength to an energy in eV */
double energyDesired;
if (energyOrWavelength != 0) energyDesired = h * c / findMe;
else energyDesired = findMe;
/* Check to make sure that the energy or wavelength passed in is within the parameters available to this method. */
if (energyDesired < 10)
throw new Exception(
"Your choice of an energy or wavelength of "
+ energyDesired
+ " is too low. \nPlease choose an energy such that "
+ "E > 10eV or a wavelength such that lambda < 1238.174 Angstroms.");
/* If the energy that is passed in is greater than 30keV or less than .413 Angstroms, return a real scattering value of the Z value and 0 for the complex scattering.
* This is a reasonable approximation. If more exact numbers are needed, please reference http://www.nist.gov/physlab/data/ffast/index.cfm */
if (energyDesired > 30000) return new JComplex(Z, 0);
/* get the abbreviation for the element based on the index i and make it lower case */
String abbreviation = elementNameAbbrev[Z - 1][0].toLowerCase();
/* find the location of the program by creating a new file "." and getting the path. Then take the substring that includes the path less the file name */
String findLocation = (new File(".").getAbsolutePath());
findLocation = findLocation.substring(0, findLocation.length() - 1);
/* Initialize the file reader */
try {
fr = new FileReader(new File(findLocation + "/sf/" + abbreviation + ".nff"));
} catch (FileNotFoundException e) {
System.out.println("Cannot find the .nff files");
e.printStackTrace();
}
/* Declare a new scanner to parse the file 'name.nff' */
Scanner s = new Scanner(fr);
/* skip the first line of the file */
if (s.next().compareTo("E(eV)") == 0) s.nextLine();
/* declare two variables to hold the current and previous values of the energy to compare them */
double energyCurrent = 0;
double energyPrevious = 0;
/* declare two JComplex numbers to hold the current and previous values of the complex scattering factors */
JComplex current = new JComplex(0., 0.);
JComplex previous = new JComplex(0., 0.);
/* if findMe is between two energies then take a percentage of the surrounding energies or wavelengths */
double howMuchOf1 = 0;
double howMuchOf2 = 0;
/* declare a boolean toggle to break out of the while loop */
boolean found = false;
/* Loop through the file as long as the desired energy has not been found*/
while (found == false) {
/* set the previous energy value to what used to be the current energy value */
energyPrevious = energyCurrent;
/* set the previous scattering factor to what used to be the current scattering factor */
previous.setRe(current.getRe());
previous.setIm(current.getIm());
/* read energy */
energyCurrent = Double.valueOf(s.next());
/* read real and imaginary parts of the scattering factor */
current.setRe(Double.valueOf(s.next()));
current.setIm(Double.valueOf(s.next()));
/* test the current energy value to the target energy value */
if (energyCurrent > energyDesired) {
/* get out of the loop */
found = true;
/* how far away is the first energy */
howMuchOf1 =
Math.abs(energyPrevious - energyDesired)
/ (Math.abs(energyPrevious - energyDesired)
+ Math.abs(energyCurrent - energyDesired));
/* how far away is the second energy */
howMuchOf2 =
Math.abs(energyCurrent - energyDesired)
/ (Math.abs(energyPrevious - energyDesired)
+ Math.abs(energyCurrent - energyDesired));
}
if (found == false) s.nextLine();
}
previous = JComplex.multiply(previous, howMuchOf1);
/* set the second complex scattering factor to be how far away from the second energy your selection is times
the complex scattering factor at the second energy */
current = JComplex.multiply(current, howMuchOf2);
/* Test to see if the first complex scattering factor is near an absorption edge */
if (previous.getRe() < -1 * Z) previous.setRe(0);
/* Test to see if the second complex scattering factor is near an absorption edge */
if (current.getRe() < -1 * Z) current.setRe(0);
/* return the complex scattering factor to be how far away from the bracketing energies your selection is times
the complex scattering factor */
return JComplex.add(previous, current);
}