/usr/include/sc/chemistry/molecule/atominfo.h is in libsc-dev 2.3.1-16.
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// atominfo.h
//
// Copyright (C) 1996 Limit Point Systems, Inc.
//
// Author: Curtis Janssen <cljanss@limitpt.com>
// Maintainer: LPS
//
// This file is part of the SC Toolkit.
//
// The SC Toolkit is free software; you can redistribute it and/or modify
// it under the terms of the GNU Library General Public License as published by
// the Free Software Foundation; either version 2, or (at your option)
// any later version.
//
// The SC Toolkit is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Library General Public License for more details.
//
// You should have received a copy of the GNU Library General Public License
// along with the SC Toolkit; see the file COPYING.LIB. If not, write to
// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
//
// The U.S. Government is granted a limited license as per AL 91-7.
//
#ifndef _chemistry_molecule_atominfo_h
#define _chemistry_molecule_atominfo_h
#include <string>
#include <map>
#include <vector>
#include <util/class/class.h>
#include <util/keyval/keyval.h>
namespace sc {
class Units;
/** The AtomInfo class provides information about atoms. The information
is kept in a file named atominfo.kv in the SC library directory. That
information can be overridden by the user. */
class AtomInfo: public SavableState {
private:
enum { Nelement = 118, DefaultZ = 0 };
struct atom
{
int Z;
char *name;
char *symbol;
};
static struct atom elements_[Nelement];
std::map<std::string,int> name_to_Z_;
std::map<std::string,int> symbol_to_Z_;
std::map<int,std::string> Z_to_names_;
std::map<int,std::string> Z_to_symbols_;
std::map<int,double> Z_to_mass_;
std::map<int,double> Z_to_atomic_radius_;
std::map<int,double> Z_to_vdw_radius_;
std::map<int,double> Z_to_bragg_radius_;
std::map<int,double> Z_to_maxprob_radius_;
std::map<int,std::vector<double> > Z_to_rgb_;
std::map<int,double> Z_to_ip_;
double atomic_radius_scale_;
double vdw_radius_scale_;
double bragg_radius_scale_;
double maxprob_radius_scale_;
char *overridden_values_;
void load_library_values();
void override_library_values(const Ref<KeyVal> &keyval);
void load_values(const Ref<KeyVal>& keyval, int override);
void load_values(std::map<int,double>&,
double *scale, const char *keyword,
const Ref<KeyVal> &keyval, int override,
const Ref<Units> &);
void load_values(std::map<int,std::vector<double> >&,
const char *keyword,
const Ref<KeyVal> &keyval, int override);
void add_overridden_value(const char *assignment);
void initialize_names();
double lookup_value(const std::map<int,double>& values, int Z) const;
double lookup_array_value(const std::map<int,std::vector<double> >& values,
int Z, int i) const;
public:
AtomInfo();
/** The AtomInfo KeyVal constructor is used to generate a AtomInfo
object from the input. Default values will be read in from the
<tt>atominfo.kv</tt> file in library directory. These can be
overridden by specifying the keyword below. The library file is
also read using a KeyVal constructor syntax, so consult that file
for an example.
<table border="1">
<tr><td>Keyword<td>Type<td>Default<td>Description
<tr><td><tt>mass:unit</tt><td>string<td><tt>amu</tt><td>The unit to
be used for masses. See the Units class for more information about
units.
<tr><td><tt>mass:</tt><em>symbol</em><td>double<td>library
value<td>The mass associated with the given atomic symbol.
<tr><td><tt>vdw_radius:unit</tt><td>string<td><tt>bohr</tt><td>The
unit to be used for van der Waals radii. See the Units class for
more information about units.
<tr><td><tt>vdw_radius:scaling_factor</tt><td>double<td>1.0<td>The
scaling factor to be used for all van der Waals radii, including
library values.
<tr><td><tt>vdw_radius:</tt><em>symbol</em><td>double<td>library
value <td>The van der Waals radius associated with the given atomic
symbol.
<tr><td><tt>atomic_radius:unit</tt><td>string<td><tt>bohr</tt><td>The
unit to be used for atomic radii. See the Units class for more
information about units.
<tr><td><tt>atomic_radius:scaling_factor</tt><td>double<td>1.0<td>The
scaling factor to be used for all atomic radii, including library
values.
<tr><td><tt>atomic_radius:</tt><em>symbol</em><td>double<td>library
value <td>The atomic radius associated with the given atomic
symbol.
<tr><td><tt>bragg_radius:unit</tt><td>string<td><tt>bohr</tt><td>The
unit to be used for Bragg radii. See the Units class for more
information about units.
<tr><td><tt>bragg_radius:scaling_factor</tt><td>double<td>1.0<td>The
scaling factor to be used for all Bragg radii, including library
values.
<tr><td><tt>bragg_radius:</tt><em>symbol</em><td>double<td>library
value <td>The Bragg radius associated with the given atomic symbol.
<tr><td><tt>maxprob_radius:unit</tt><td>string<td><tt>bohr</tt><td>The
unit to be used for maximum probability radii. See the Units class
for more information about units.
<tr><td><tt>maxprob_radius:scaling_factor</tt><td>double<td>1.0<td>The
scaling factor to be used for all maximum probability radii,
including library values.
<tr><td><tt>maxprob_radius:</tt><em>symbol</em><td>double<td>library
value<td>The maximum probability radius associated with the given
atomic symbol.
<tr><td><tt>ip:unit</tt><td>string<td><tt>Hartree</tt><td>The unit
to be used for ionization potentials. See the Units class for more
information about units.
<tr><td><tt>ip:</tt><em>symbol</em><td>double<td>library
value<td>The ionization potential for the given atom.
<tr><td><tt>rgb:</tt><em>symbol</em><td>double[3]<td>library
value<td>A vector with the red, green, and blue values used to
color each atom. Each element is between 0 (off) and 1 (on).
</table>
*/
AtomInfo(const Ref<KeyVal>&);
AtomInfo(StateIn&);
~AtomInfo();
void save_data_state(StateOut& s);
/// These return various measures of the atom's radius.
double vdw_radius(int Z) const;
double bragg_radius(int Z) const;
double atomic_radius(int Z) const;
double maxprob_radius(int Z) const;
/// Returns the atomization potential for atomic number Z.
double ip(int Z) const;
/// Return the scale factor for the VdW radii.
double vdw_radius_scale() const { return vdw_radius_scale_; }
/// Return the scale factor for the Bragg radii.
double bragg_radius_scale() const { return bragg_radius_scale_; }
/// Return the scale factor for the atomic radii.
double atomic_radius_scale() const { return atomic_radius_scale_; }
/// Return the scale factor for the maximum probability radii.
double maxprob_radius_scale() const { return maxprob_radius_scale_; }
/** These return information about the color of the atom
for visualization programs. */
double rgb(int Z, int color) const;
double red(int Z) const;
double green(int Z) const;
double blue(int Z) const;
/// This returns the mass of the most abundant isotope.
double mass(int Z) const;
/// This returns the full name of the element.
std::string name(int Z);
/// This returns the symbol for the element.
std::string symbol(int Z);
/// This converts a name or symbol to the atomic number.
int string_to_Z(const std::string &, int allow_exceptions = 1);
};
}
#endif
// Local Variables:
// mode: c++
// c-file-style: "CLJ"
// End:
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