#ifndef CCTBX_ELTBX_XRAY_SCATTERING_H #define CCTBX_ELTBX_XRAY_SCATTERING_H #include #include #include #include #include #include namespace cctbx { namespace eltbx { namespace xray_scattering { static const char *standard_labels[] = { "H", "D", "T", "Hiso", "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", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "H1-", "D1-", "T1-", "Li1+", "Be2+", "Cval", "O1-", "O2-", "F1-", "Na1+", "Mg2+", "Al3+", "Sival", "Si4+", "Cl1-", "K1+", "Ca2+", "Sc3+", "Ti2+", "Ti3+", "Ti4+", "V2+", "V3+", "V5+", "Cr2+", "Cr3+", "Mn2+", "Mn3+", "Mn4+", "Fe2+", "Fe3+", "Co2+", "Co3+", "Ni2+", "Ni3+", "Cu1+", "Cu2+", "Zn2+", "Ga3+", "Ge4+", "Br1-", "Rb1+", "Sr2+", "Y3+", "Zr4+", "Nb3+", "Nb5+", "Mo3+", "Mo5+", "Mo6+", "Ru3+", "Ru4+", "Rh3+", "Rh4+", "Pd2+", "Pd4+", "Ag1+", "Ag2+", "Cd2+", "In3+", "Sn2+", "Sn4+", "Sb3+", "Sb5+", "I1-", "Cs1+", "Ba2+", "La3+", "Ce3+", "Ce4+", "Pr3+", "Pr4+", "Nd3+", "Pm3+", "Sm3+", "Eu2+", "Eu3+", "Gd3+", "Tb3+", "Dy3+", "Ho3+", "Er3+", "Tm3+", "Yb2+", "Yb3+", "Lu3+", "Hf4+", "Ta5+", "W6+", "Os4+", "Ir3+", "Ir4+", "Pt2+", "Pt4+", "Au1+", "Au3+", "Hg1+", "Hg2+", "Tl1+", "Tl3+", "Pb2+", "Pb4+", "Bi3+", "Bi5+", "Ra2+", "Ac3+", "Th4+", "U3+", "U4+", "U6+", "Np3+", "Np4+", "Np6+", "Pu3+", "Pu4+", "Pu6+", 0 }; inline bool is_reserved_scattering_type_label( std::string const& label) { if (label == "const") return true; if (label == "AX" || label == "TX" || label == "XX") return true; if (label == "unknown") return true; return false; } inline void throw_if_reserved_scattering_type_label( std::string const& label) { if (is_reserved_scattering_type_label(label)) { throw std::invalid_argument( "Reserved scattering type label: \""+label+"\""); } } inline boost::optional get_standard_label( std::string const& label, bool exact=false, bool optional=false) { if (label == "const") return boost::optional(label); if (label == "AX" || label == "TX" || label == "XX") return boost::optional(label); std::string work_label = basic::strip_label(label, exact); const char* result = 0; int m = 0; for (const char **std_lbl = standard_labels; *std_lbl; std_lbl++) { int i = basic::match_labels(work_label, *std_lbl); if (i < 0 /* exact match */) { return boost::optional(*std_lbl); } if (i > m && !isdigit((*std_lbl)[i-1])) { m = i; result = *std_lbl; } } if (exact || result == 0) { if (optional) return boost::optional(); throw std::invalid_argument( "Unknown scattering type label: \"" + label + "\""); } return boost::optional(result); } inline std::string replace_hydrogen_isotype_labels(std::string standard_label) { if (standard_label == "D" || standard_label == "T" ) return "H"; else if (standard_label == "D1-" || standard_label == "T1-") return "H1-"; return standard_label; } namespace detail { static const float undefined = -99999.; template struct raw_table_entry { const char* label; float a[N], b[N], c; }; } //! Coefficients for the Analytical Approximation to the Scattering Factor. /*! Used to work with coefficients from the International Tables Volume C (1992) (template parameter N = 4) and Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431 (template parameter N = 5). */ template class base { public: //! Default constructor. Calling certain methods may cause crashes! base() : table_(0), entry_(0) {} //! Constructor. For internal use only. base(const detail::raw_table_entry* table_raw, const char* table, std::string const& label, bool exact); //! Tests if the instance is constructed properly. /*! Shorthand for: label() != 0

Not available in Python. */ bool is_valid() const { return entry_->label != 0; } //! Label of table. Either "IT1992" or "WK1995". const char* table() const { return table_; } //! Scattering factor label. E.g. "Si4+". const char* label() const { return entry_->label; } //! Fetches the Gaussian terms from the static table. gaussian fetch() const { typedef af::small small_t; return gaussian( small_t(entry_->a, entry_->a+N), small_t(entry_->b, entry_->b+N), entry_->c, true); } protected: const char *table_; const detail::raw_table_entry* entry_; void next_entry(); }; // non-inline constructor template base::base(const detail::raw_table_entry* table_raw, const char* table, std::string const& label, bool exact) : table_(table), entry_(0) { throw_if_reserved_scattering_type_label(label); std::string std_lbl = replace_hydrogen_isotype_labels( *get_standard_label(label, exact)); for (const detail::raw_table_entry* entry = table_raw; entry->label; entry++) { if (entry->label == std_lbl) { entry_ = entry; break; } } if (entry_ == 0) { throw std::invalid_argument( "Unknown scattering type label: \"" + label + "\""); } } // non-inline member function template void base::next_entry() { if (is_valid()) entry_++; } //! Coefficients for the Analytical Approximation to the Scattering Factor. /*! Coefficients from the International Tables for Crystallography, Volume C, Mathematical, Physical and Chemical Tables, Edited by A.J.C. Wilson, Kluwer Academic Publishers, Dordrecht/Boston/London, 1992.

Table 6.1.1.4 (pp. 500-502): Coefficients for analytical approximation to the scattering factors of Tables 6.1.1.1 and 6.1.1.3.

Table 6.1.1.4 is a reprint of Table 2.2B, pp. 99-101, International Tables for X-ray Crystallography, Volume IV, The Kynoch Press: Birmingham, England, 1974. There is just one difference for Tl3+:

                IT Vol IV 1974: a2 = 18.3841
                IT Vol C  1992: a2 = 18.3481

The value from IT Vol IV is presumed to be the correct one and used here.

If possible, the class xray_scattering::wk1995 should be used instead of this class. The coefficients of Waasmaier & Kirfel give more precise approximations than the coefficients of Volume C and some errors are corrected.

See also: xray_scattering::it1992_iterator, xray_scattering::wk1995, xray_scattering::base */ class it1992: public base<4> { public: //! Facilitates meta-programming. typedef base<4> base_type; //! Default constructor. Calling certain methods may cause crashes! it1992() {} //! Looks up coefficients for the given scattering factor label. /*! If exact == true, the scattering factor label must exactly match the tabulated label. However, the lookup is not case-sensitive.
E.g., "SI4" will be matched with "Si".
"Si4+" and "Si+4" will be matched with "Si4+".
See also: eltbx::basic::strip_label()

Note that the other methods of this class are inherited from class xray_scattering::base. */ it1992(std::string const& label, bool exact=false); protected: friend class it1992_iterator; }; /*! \brief Iterator over table of Coefficients for the Analytical Approximation to the Scattering Factor, International Tables 1992. */ class it1992_iterator { public: //! Initialization of the iterator. it1992_iterator(); //! Retrieves the next entry from the internal table. /*! Use it1992::is_valid() to detect end-of-iteration. */ it1992 next(); private: it1992 current_; }; //! Coefficients for the Analytical Approximation to the Scattering Factor. /*! Coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431.

The original data can be found at: 

      ftp://wrzx02.rz.uni-wuerzburg.de/pub/local/Crystallography/sfac.dat
File picked up Jul 4, 1995. File verified Sep 12, 2001.

Header of "sfac.dat": 

        - Fitparameters of all atoms/ions (with the excepetion of O1-)
          from publication "New Analytical Scattering Factor Functions
          for Free Atoms and Ions", D. Waasmaier & A. Kirfel, Acta Cryst.
          A 1995, in press)

        - Fit for O1- based on the tabulated values of Table 2 (D.REZ,
          P.REZ & I.GRANT, Acta Cryst. (1994), A50, 481-497).

        - Fits for all other atoms/ions based on the tabulated values
          of Table 6.1.1.1 (atoms) and Table 6.1.1.3 (ions)
          (International Tables for Crystallography, Vol. C, 1992).

See also: xray_scattering::wk1995_iterator, xray_scattering::it1992, xray_scattering::base */ class wk1995: public base<5> { public: //! Facilitates meta-programming. typedef base<5> base_type; //! Default constructor. Calling certain methods may cause crashes! wk1995() {} //! Looks up coefficients for the given scattering factor label. /*! If exact == true, the scattering factor label must exactly match the tabulated label. However, the lookup is not case-sensitive.
E.g., "SI4" will be matched with "Si".
"Si4+" and "Si+4" will be matched with "Si4+".
See also: eltbx::basic::strip_label()

Note that the other methods of this class are inherited from class base. */ wk1995(std::string const& label, bool exact=false); protected: friend class wk1995_iterator; }; /*! \brief Iterator over table of Coefficients for the Analytical Approximation to the Scattering Factor, Waasmaier & Kirfel 1995. */ class wk1995_iterator { public: //! Initialization of the iterator. wk1995_iterator(); //! Retrieves the next entry from the internal table. /*! Use wk1995::is_valid() to detect end-of-iteration. */ wk1995 next(); private: wk1995 current_; }; }}} // cctbx::eltbx::xray_scattering #endif // CCTBX_ELTBX_XRAY_SCATTERING_H