simple.h

/* simple.h -- definition of the simple internal coordinate classes
 *
 *      THIS SOFTWARE FITS THE DESCRIPTION IN THE U.S. COPYRIGHT ACT OF A
 *      "UNITED STATES GOVERNMENT WORK".  IT WAS WRITTEN AS A PART OF THE
 *      AUTHOR'S OFFICIAL DUTIES AS A GOVERNMENT EMPLOYEE.  THIS MEANS IT
 *      CANNOT BE COPYRIGHTED.  THIS SOFTWARE IS FREELY AVAILABLE TO THE
 *      PUBLIC FOR USE WITHOUT A COPYRIGHT NOTICE, AND THERE ARE NO
 *      RESTRICTIONS ON ITS USE, NOW OR SUBSEQUENTLY.
 *
 *  Author:
 *      E. T. Seidl
 *      Bldg. 12A, Rm. 2033
 *      Computer Systems Laboratory
 *      Division of Computer Research and Technology
 *      National Institutes of Health
 *      Bethesda, Maryland 20892
 *      Internet: seidl@alw.nih.gov
 *      February, 1993
 */
 
#ifndef _intco_simple_h
#define _intco_simple_h
 
 
#include <iostream>
 
#include <util/class/class.h>
#include <util/state/state.h>
#include <util/keyval/keyval.h>
#include <chemistry/molecule/molecule.h>
#include <chemistry/molecule/coor.h>
 
#include <math/scmat/vector3.h>
 
namespace sc {
 
// ////////////////////////////////////////////////////////////////////////
 
 
class SimpleCo : public IntCoor {
  protected:
    int natoms_;
    int *atoms;
 
  public:
    SimpleCo();
    SimpleCo(int,const char* =0);
    SimpleCo(const Ref<KeyVal>&,int natom);
 
    virtual ~SimpleCo();
 
    int natoms() const;
    int operator[](int i) const;
 
    void save_data_state(StateOut&);
    SimpleCo(StateIn&);
 
    virtual int operator==(SimpleCo&);
    int operator!=(SimpleCo&u);
 
    // these IntCoor members are implemented in term of
    // the calc_force_con and calc_intco members.
    double force_constant(Ref<Molecule>&);
    void update_value(const Ref<Molecule>&);
    void bmat(const Ref<Molecule>&,RefSCVector&bmat,double coef = 1.0);
 
    virtual double calc_force_con(Molecule&) = 0;
    virtual double calc_intco(Molecule&, double* =0, double =1) = 0;
 
    void print_details(const Ref<Molecule> &,
                       std::ostream& = ExEnv::out0()) const;
    
    int equivalent(Ref<IntCoor>&);
  };
 
// ///////////////////////////////////////////////////////////////////////
 
#define SimpleCo_DECLARE(classname)                       \
  public:                                     \
    virtual classname& operator=(const classname&);               \
    SimpleCo& operator=(const SimpleCo&);                     \
    double calc_force_con(Molecule&);                         \
    double calc_intco(Molecule&, double* =0, double =1);              \
    classname(StateIn&);                              \
    void save_data_state(StateOut&)
 
#define SimpleCo_IMPL_eq(classname)                       \
SimpleCo& classname::operator=(const SimpleCo& c)                 \
{                                         \
  classname *cp = dynamic_cast<classname*>((SimpleCo*)&c);                \
  if(cp) {                                    \
      *this=*cp;                                  \
    }                                         \
  else {                                      \
      natoms_ = 0;                                \
      atoms = 0;                                  \
    }                                         \
                                          \
  return *this;                                   \
  }
 
#define SimpleCo_IMPL_StateIn(classname)                      \
classname::classname(StateIn&si):                         \
  SimpleCo(si)                                    \
{                                         \
}
 
#define SimpleCo_IMPL_save_data_state(classname)                  \
void classname::save_data_state(StateOut&so)                      \
{                                         \
  SimpleCo::save_data_state(so);                          \
}
 
#define SimpleCo_IMPL(classname)        \
        SimpleCo_IMPL_eq(classname)     \
        SimpleCo_IMPL_StateIn(classname)    \
        SimpleCo_IMPL_save_data_state(classname)
 
// ///////////////////////////////////////////////////////////////////////
 
class StreSimpleCo : public SimpleCo {
    SimpleCo_DECLARE(StreSimpleCo);
  public:
    StreSimpleCo();
    StreSimpleCo(const StreSimpleCo&);
    StreSimpleCo(const char*, int, int);
    StreSimpleCo(const Ref<KeyVal>&);
 
    ~StreSimpleCo();
 
    const char * ctype() const;
 
    double bohr() const;
    double angstrom() const;
    double preferred_value() const;
  };
 
typedef StreSimpleCo Stre;
 
// ///////////////////////////////////////////////////////////////////////
 
static const double rtd = 180.0/M_PI;
 
class BendSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(BendSimpleCo);
  public:
    BendSimpleCo();
    BendSimpleCo(const BendSimpleCo&);
    BendSimpleCo(const char*, int, int, int);
    BendSimpleCo(const Ref<KeyVal>&);
 
    ~BendSimpleCo();
 
    const char * ctype() const;
    
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef BendSimpleCo Bend;
 
// ///////////////////////////////////////////////////////////////////////
 
class TorsSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(TorsSimpleCo);
  public:
    TorsSimpleCo();
    TorsSimpleCo(const TorsSimpleCo&);
    TorsSimpleCo(const char *refr, int, int, int, int);
    TorsSimpleCo(const Ref<KeyVal>&);
 
    ~TorsSimpleCo();
 
    const char * ctype() const;
    
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef TorsSimpleCo Tors;
 
// ///////////////////////////////////////////////////////////////////////
 
class ScaledTorsSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(ScaledTorsSimpleCo);
  private:
    double old_torsion_;
  public:
    ScaledTorsSimpleCo();
    ScaledTorsSimpleCo(const ScaledTorsSimpleCo&);
    ScaledTorsSimpleCo(const char *refr, int, int, int, int);
    ScaledTorsSimpleCo(const Ref<KeyVal>&);
 
    ~ScaledTorsSimpleCo();
 
    const char * ctype() const;
    
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef ScaledTorsSimpleCo ScaledTors;
 
// ///////////////////////////////////////////////////////////////////////
 
/*
The OutSimpleCo class describes an out-of-plane internal coordinate
of a molecule.  The input is described in the documentation of its parent
class SimpleCo.
 
Designating the four atoms as \f$a\f$, \f$b\f$, \f$c\f$, and \f$d\f$ and
their cartesian positions as \f$\bar{r}_a\f$, \f$\bar{r}_b\f$,
\f$\bar{r}_c\f$, and \f$\bar{r}_d\f$, the value of the coordinate,
\f$\tau\f$, is given by
 
\f[ \bar{u}_{ab} = \frac{\bar{r}_a - \bar{r}_b}{\| \bar{r}_a - \bar{r}_b \|}\f]
\f[ \bar{u}_{cb} = \frac{\bar{r}_b - \bar{r}_c}{\| \bar{r}_c - \bar{r}_b \|}\f]
\f[ \bar{u}_{db} = \frac{\bar{r}_c - \bar{r}_d}{\| \bar{r}_c - \bar{r}_b \|}\f]
\f[ \bar{n}_{bcd}= \frac{\bar{u}_{cb} \times \bar{u}_{db}}
                     {\| \bar{u}_{cb} \times \bar{u}_{db} \|}\f]
\f[ \phi         = \arcsin ( \bar{u}_{ab} \cdot \bar{n}_{bcd} )\f]
 
*/
class OutSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(OutSimpleCo);
  public:
    OutSimpleCo();
    OutSimpleCo(const OutSimpleCo&);
    OutSimpleCo(const char *refr, int, int, int, int);
    OutSimpleCo(const Ref<KeyVal>&);
 
    ~OutSimpleCo();
 
    const char * ctype() const;
    
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef OutSimpleCo Out;
 
// ///////////////////////////////////////////////////////////////////////
 
class LinIPSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(LinIPSimpleCo);
  private:
    SCVector3 u2;
  public:
    LinIPSimpleCo();
    LinIPSimpleCo(const LinIPSimpleCo&);
    LinIPSimpleCo(const char *refr, int, int, int, const SCVector3 &u);
    LinIPSimpleCo(const Ref<KeyVal>&);
 
    ~LinIPSimpleCo();
 
    const char * ctype() const;
 
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef LinIPSimpleCo LinIP;
 
// ///////////////////////////////////////////////////////////////////////
 
class LinOPSimpleCo : public SimpleCo { 
    SimpleCo_DECLARE(LinOPSimpleCo);
  private:
    SCVector3 u2;
  public:
    LinOPSimpleCo();
    LinOPSimpleCo(const LinOPSimpleCo&);
    LinOPSimpleCo(const char *refr, int, int, int, const SCVector3 &u);
    LinOPSimpleCo(const Ref<KeyVal>&);
 
    ~LinOPSimpleCo();
 
    const char * ctype() const;
 
    double radians() const;
    double degrees() const;
    double preferred_value() const;
  };
 
typedef LinOPSimpleCo LinOP;
 
// end of addtogroup ChemistryMolecule
 
}
 
#endif /* _intco_simple_h */
 
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