Material.cpp

//------------------------------------------------------------------------------
// Includes
//------------------------------------------------------------------------------
#include "MantidKernel/Material.h"
#include "MantidKernel/Atom.h"
#include <boost/lexical_cast.hpp>
#include <boost/make_shared.hpp>
#include <boost/regex.hpp>
#include <boost/tokenizer.hpp>
#include <sstream>
#include <stdexcept>
#include <utility>

namespace Mantid
{

  namespace Kernel
  {
    typedef boost::tokenizer<boost::char_separator<char> >  tokenizer;
    typedef std::pair<std::string, std::string> str_pair;

    using PhysicalConstants::Atom;
    using PhysicalConstants::getAtom;
    using PhysicalConstants::NeutronAtom;

    /**
     * Construct an "empty" material. Everything returns zero
     */
    Material::Material() : 
      m_name(), m_element(0,0,0.0,0.0,0.0,0.0,0.0,0.0),
      m_numberDensity(0.0), m_temperature(0.0), m_pressure(0.0)
    {
    }

    /**
    * Construct a material object
    * @param name :: The name of the material
    * @param element :: The element it is composed from
    * @param numberDensity :: Density in A^-3
    * @param temperature :: The temperature in Kelvin (Default = 300K)
    * @param pressure :: Pressure in kPa (Default: 101.325 kPa)
    */
    Material::Material(const std::string & name, const PhysicalConstants::NeutronAtom& element,
		       const double numberDensity, const double temperature, 
		       const double pressure) :
      m_name(name), m_element(element), m_numberDensity(numberDensity), 
      m_temperature(temperature), m_pressure(pressure)
    {
    }   
    
    /** 
     * Returns the name 
     * @returns A string containing the name of the material
     */
    const std::string & Material::name() const 
    { 
      return m_name; 
    }

    /** 
     * Get the number density
     * @returns The number density of the material in A^-3
     */
    double Material::numberDensity() const
    { 
      return m_numberDensity; 
    }
    
    /** 
     * Get the temperature
     * @returns The temperature of the material in Kelvin
     */
    double Material::temperature() const 
    { 
      return m_temperature; 
    }
    
    /** 
     * Get the pressure
     * @returns The pressure of the material
     */
    double Material::pressure() const
    { 
      return m_pressure; 
    }

    /**
     * Get the coherent scattering cross section for a given wavelength.
     * CURRENTLY this simply returns the value for the underlying element
     * @param lambda :: The wavelength to evaluate the cross section
     * @returns The value of the coherent scattering cross section at 
     * the given wavelength
     */ 
    double Material::cohScatterXSection(const double lambda) const
    {
      (void)lambda;
      return m_element.coh_scatt_xs;
      
    }
    
    /**
     * Get the incoherent scattering cross section for a given wavelength
     * CURRENTLY this simply returns the value for the underlying element
     * @param lambda :: The wavelength to evaluate the cross section
     * @returns The value of the coherent scattering cross section at 
     * the given wavelength
     */
    double Material::incohScatterXSection(const double lambda) const
    {
      (void)lambda;
      return m_element.inc_scatt_xs;
    }

    /**
     * Get the total scattering cross section for a given wavelength
     * CURRENTLY this simply returns the value for sum of the incoherent
     * and coherent scattering cross sections.
     * @param lambda :: The wavelength to evaluate the cross section
     * @returns The value of the total scattering cross section at 
     * the given wavelength
     */
    double Material::totalScatterXSection(const double lambda) const
    {
      UNUSED_ARG(lambda);
      return m_element.tot_scatt_xs;
    }

    /**
     * Get the absorption cross section for a given wavelength.
     * CURRENTLY This assumes a linear dependence on the wavelength with the reference
     * wavelength = NeutronAtom::ReferenceLambda angstroms.
     * @param lambda :: The wavelength to evaluate the cross section
     * @returns The value of the absoprtioncross section at 
     * the given wavelength
     */
    double Material::absorbXSection(const double lambda) const
    {
      return (m_element.abs_scatt_xs) * (lambda / NeutronAtom::ReferenceLambda);
    }


    /** Save the object to an open NeXus file.
     * @param file :: open NeXus file
     * @param group :: name of the group to create
     */
    void Material::saveNexus(::NeXus::File * file, const std::string & group) const
    {
      file->makeGroup(group, "NXdata", 1);
      file->putAttr("version", 1);
      file->putAttr("name", m_name);
      file->writeData("element_Z", m_element.z_number);
      file->writeData("element_A", m_element.a_number);
      file->writeData("number_density", m_numberDensity);
      file->writeData("temperature", m_temperature);
      file->writeData("pressure", m_pressure);
      file->closeGroup();
    }

    /** Load the object from an open NeXus file.
     * @param file :: open NeXus file
     * @param group :: name of the group to open
     */
    void Material::loadNexus(::NeXus::File * file, const std::string & group)
    {
      file->openGroup(group, "NXdata");
      file->getAttr("name", m_name);

      // Find the element
      uint16_t element_Z, element_A;
      file->readData("element_Z", element_Z);
      file->readData("element_A", element_A);
      try {
      m_element = Mantid::PhysicalConstants::getNeutronAtom(element_Z, element_A);
      }
      catch (std::runtime_error &)
      { /* ignore and use the default */ }

      file->readData("number_density", m_numberDensity);
      file->readData("temperature", m_temperature);
      file->readData("pressure", m_pressure);
      file->closeGroup();
    }

    namespace { // anonymous namespace to hide the function
    str_pair getAtomName(std::string &text) // TODO change to get number after letters
    {
        // one character doesn't need
        if (text.size() <= 1)
            return std::make_pair(text, "");

        // check the second character
        const char *s;
        s = text.c_str();
        if ((s[1] >= '0' && s[1]<='9') || s[1] == '.')
            return std::make_pair(text.substr(0,1), text.substr(1));
        else
            return std::make_pair(text.substr(0,2), text.substr(2));
    }
    }

    Material::ChemicalFormula Material::parseChemicalFormula(const std::string chemicalSymbol)
    {
      Material::ChemicalFormula CF;

      const boost::char_separator<char> ATOM_DELIM(" -");
      tokenizer tokens(chemicalSymbol, ATOM_DELIM);
      for (auto atom = tokens.begin(); atom != tokens.end(); ++atom)
      {
          try {
              std::string name(*atom);
              float numberAtoms = 1;
              uint16_t aNumber = 0;

              // split out the isotope bit
              if (atom->find('(') != std::string::npos)
              {
                  // error check
                  size_t end = atom->find(')');
                  if (end == std::string::npos)
                  {
                      std::stringstream msg;
                      msg << "Failed to parse isotope \"" << name << "\"";
                      throw std::runtime_error(msg.str());
                  }

                  // get the number of atoms
                  std::string numberAtomsStr = name.substr(end+1);
                  if (!numberAtomsStr.empty())
                      numberAtoms = boost::lexical_cast<float>(numberAtomsStr);

                  // split up the atom and isotope number
                  name = name.substr(1, end-1);
                  str_pair temp = getAtomName(name);

                  name = temp.first;
                  aNumber = boost::lexical_cast<uint16_t>(temp.second);
              }
              else // for non-isotopes
              {
                  str_pair temp = getAtomName(name);
                  name = temp.first;
                  if (!temp.second.empty())
                      numberAtoms = boost::lexical_cast<float>(temp.second);
              }

              CF.atoms.push_back(boost::make_shared<Atom>(getAtom(name, aNumber)));
              CF.numberAtoms.push_back(numberAtoms);
          }
          catch (boost::bad_lexical_cast &e)
          {
              std::stringstream msg;
              msg << "While trying to parse atom \"" << (*atom)
                  << "\" encountered bad_lexical_cast: " << e.what();
              throw std::runtime_error(msg.str());
          }
      }

      return CF;
    }
  }

}