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coor.h // // coor.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_coor_h #define _chemistry_molecule_coor_h #ifdef __GNUC__ #pragma interface #endif #include <iostream> #include <vector> #include <math/scmat/matrix.h> #include <math/optimize/transform.h> #include <chemistry/molecule/molecule.h> namespace sc { class IntCoor: public SavableState { protected: // conversion factors from radians, bohr to the preferred units static double bohr_conv; static double radian_conv; char *label_; double value_; public: IntCoor(StateIn&); IntCoor(const IntCoor&); IntCoor(const char* label = 0); IntCoor(const Ref<KeyVal>&); virtual ~IntCoor(); void save_data_state(StateOut&); virtual const char* label() const; virtual double value() const; virtual void set_value(double); virtual double preferred_value() const; virtual const char* ctype() const = 0; virtual void print(std::ostream & o=ExEnv::out0()) const; virtual void print_details(const Ref<Molecule> &, std::ostream& =ExEnv::out0()) const; virtual double force_constant(Ref<Molecule>&) = 0; virtual void update_value(const Ref<Molecule>&) = 0; virtual void bmat(const Ref<Molecule>&,RefSCVector&bmat,double coef=1.0) = 0; virtual int equivalent(Ref<IntCoor>&) = 0; }; class SumIntCoor: public IntCoor { private: std::vector<double> coef_; std::vector<Ref<IntCoor> > coor_; public: SumIntCoor(StateIn&); SumIntCoor(const char *); SumIntCoor(const Ref<KeyVal>&); ~SumIntCoor(); void save_data_state(StateOut&); int n(); void add(Ref<IntCoor>&,double coef); void normalize(); // IntCoor overrides double preferred_value() const; const char* ctype() const; void print_details(const Ref<Molecule> &, std::ostream& =ExEnv::out0()) const; double force_constant(Ref<Molecule>&); void update_value(const Ref<Molecule>&); void bmat(const Ref<Molecule>&,RefSCVector&bmat,double coef = 1.0); int equivalent(Ref<IntCoor>&); }; class SetIntCoor: public SavableState { private: std::vector<Ref<IntCoor> > coor_; public: SetIntCoor(); SetIntCoor(StateIn&); SetIntCoor(const Ref<KeyVal>&); virtual ~SetIntCoor(); void save_data_state(StateOut&); void add(const Ref<IntCoor>&); void add(const Ref<SetIntCoor>&); void pop(); void clear(); int n() const; Ref<IntCoor> coor(int i) const; virtual void fd_bmat(const Ref<Molecule>&,RefSCMatrix&); virtual void bmat(const Ref<Molecule>&, RefSCMatrix&); virtual void guess_hessian(Ref<Molecule>&,RefSymmSCMatrix&); virtual void print_details(const Ref<Molecule> &,std::ostream& =ExEnv::out0()) const; virtual void update_values(const Ref<Molecule>&); virtual void values_to_vector(const RefSCVector&); }; // //////////////////////////////////////////////////////////////////////// class BitArrayLTri; class IntCoorGen: public SavableState { protected: Ref<Molecule> molecule_; int linear_bends_; int linear_lbends_; int linear_tors_; int linear_stors_; int nextra_bonds_; int *extra_bonds_; double linear_bend_thres_; double linear_tors_thres_; double radius_scale_factor_; void init_constants(); double cos_ijk(Molecule& m, int i, int j, int k); int hterminal(Molecule& m, BitArrayLTri& bonds, int i); int nearest_contact(int i, Molecule& m); void add_bonds(const Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m); void add_bends(const Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m); void add_tors(const Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m); void add_out(const Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m); public: IntCoorGen(const Ref<Molecule>&, int nextra=0, int *extra=0); IntCoorGen(const Ref<KeyVal>&); IntCoorGen(StateIn&); ~IntCoorGen(); void save_data_state(StateOut&); virtual void generate(const Ref<SetIntCoor>&); virtual void print(std::ostream& out=ExEnv::out0()) const; }; // //////////////////////////////////////////////////////////////////////// class MolecularCoor: public SavableState { protected: Ref<Molecule> molecule_; RefSCDimension dnatom3_; // the number of atoms x 3 Ref<SCMatrixKit> matrixkit_; // used to construct matrices int debug_; public: MolecularCoor(Ref<Molecule>&); MolecularCoor(StateIn&); MolecularCoor(const Ref<KeyVal>&); virtual ~MolecularCoor(); void save_data_state(StateOut&); RefSCDimension dim_natom3() { return dnatom3_; } Ref<Molecule> molecule() const { return molecule_; } virtual void print(std::ostream& =ExEnv::out0()) const = 0; virtual void print_simples(std::ostream& =ExEnv::out0()) const = 0; virtual RefSCDimension dim() = 0; int to_cartesian(const RefSCVector&internal); virtual int to_cartesian(const Ref<Molecule>&mol, const RefSCVector&internal) = 0; virtual int to_internal(RefSCVector&internal) = 0; virtual int to_cartesian(RefSCVector&cartesian,RefSCVector&internal) = 0; virtual int to_internal(RefSCVector&internal,RefSCVector&cartesian) = 0; virtual int to_cartesian(RefSymmSCMatrix&cartesian, RefSymmSCMatrix&internal) =0; virtual int to_internal(RefSymmSCMatrix&internal, RefSymmSCMatrix&cartesian) = 0; virtual void guess_hessian(RefSymmSCMatrix&hessian) = 0; virtual RefSymmSCMatrix inverse_hessian(RefSymmSCMatrix&) = 0; virtual int nconstrained(); virtual Ref<NonlinearTransform> change_coordinates(); Ref<SCMatrixKit> matrixkit() const { return matrixkit_; } }; class IntMolecularCoor: public MolecularCoor { protected: Ref<IntCoorGen> generator_; void form_K_matrix(RefSCDimension& dredundant, RefSCDimension& dfixed, RefSCMatrix& K, int*& is_totally_symmetric); RefSCDimension dim_; // corresponds to the number of variable coordinates RefSCDimension dvc_; // the number of variable + constant coordinates Ref<SetIntCoor> variable_; // the variable internal coordinates Ref<SetIntCoor> constant_; // the constant internal coordinates Ref<SetIntCoor> fixed_; Ref<SetIntCoor> watched_; Ref<IntCoor> followed_; // these are all of the basic coordinates Ref<SetIntCoor> bonds_; Ref<SetIntCoor> bends_; Ref<SetIntCoor> tors_; Ref<SetIntCoor> outs_; // these are provided by the user or generated coordinates that // could not be assigned to any of the above catagories Ref<SetIntCoor> extras_; Ref<SetIntCoor> all_; // Useful relationships // variable_->n() + constant_->n() = 3N-6(5) // symm_->n() + asymm_->n() = 3N-6(5) int update_bmat_; // if 1 recompute the b matrix during to_cartesian int only_totally_symmetric_; // only coors with tot. symm comp. are varied double symmetry_tolerance_; // tol used to find coors with tot. sym. comp. double simple_tolerance_; // tol used to see if a simple is included double coordinate_tolerance_; // tol used to see if a coor is included double cartesian_tolerance_; // tol used in intco->cart transformation double scale_bonds_; // scale factor for bonds double scale_bends_; // scale factor for bends double scale_tors_; // scale factor for tors double scale_outs_; // scale factor for outs int nextra_bonds_; int* extra_bonds_; int given_fixed_values_; // if true make molecule have given fixed values int decouple_bonds_; int decouple_bends_; int max_update_steps_; double max_update_disp_; virtual void init(); virtual void new_coords(); virtual void read_keyval(const Ref<KeyVal>&); // control whether or not to print coordinates when they are formed int form_print_simples_; int form_print_variable_; int form_print_constant_; int form_print_molecule_; public: IntMolecularCoor(StateIn&); IntMolecularCoor(Ref<Molecule>&mol); IntMolecularCoor(const Ref<KeyVal>&); virtual ~IntMolecularCoor(); void save_data_state(StateOut&); virtual void form_coordinates(int keep_variable=0) =0; virtual int all_to_cartesian(const Ref<Molecule> &,RefSCVector&internal); virtual int all_to_internal(const Ref<Molecule> &,RefSCVector&internal); virtual RefSCDimension dim(); virtual int to_cartesian(const Ref<Molecule> &,const RefSCVector&internal); virtual int to_internal(RefSCVector&internal); virtual int to_cartesian(RefSCVector&cartesian,RefSCVector&internal); virtual int to_internal(RefSCVector&internal,RefSCVector&cartesian); virtual int to_cartesian(RefSymmSCMatrix&cart,RefSymmSCMatrix&internal); virtual int to_internal(RefSymmSCMatrix&internal,RefSymmSCMatrix&cart); virtual void print(std::ostream& =ExEnv::out0()) const; virtual void print_simples(std::ostream& =ExEnv::out0()) const; virtual void print_variable(std::ostream& =ExEnv::out0()) const; virtual void print_constant(std::ostream& =ExEnv::out0()) const; int nconstrained(); }; // /////////////////////////////////////////////////////////////////////// class SymmMolecularCoor: public IntMolecularCoor { protected: // true if coordinates should be changed during optimization int change_coordinates_; // true if hessian should be transformed too (should always be true) int transform_hessian_; // max value for the condition number if coordinates can be changed double max_kappa2_; void init(); public: SymmMolecularCoor(Ref<Molecule>&mol); SymmMolecularCoor(StateIn&); SymmMolecularCoor(const Ref<KeyVal>&); virtual ~SymmMolecularCoor(); void save_data_state(StateOut&); void form_coordinates(int keep_variable=0); void guess_hessian(RefSymmSCMatrix&hessian); RefSymmSCMatrix inverse_hessian(RefSymmSCMatrix&); Ref<NonlinearTransform> change_coordinates(); void print(std::ostream& =ExEnv::out0()) const; }; // /////////////////////////////////////////////////////////////////////// class RedundMolecularCoor: public IntMolecularCoor { public: RedundMolecularCoor(Ref<Molecule>&mol); RedundMolecularCoor(StateIn&); RedundMolecularCoor(const Ref<KeyVal>&); virtual ~RedundMolecularCoor(); void save_data_state(StateOut&); void form_coordinates(int keep_variable=0); void guess_hessian(RefSymmSCMatrix&hessian); RefSymmSCMatrix inverse_hessian(RefSymmSCMatrix&); }; // /////////////////////////////////////////////////////////////////////// class CartMolecularCoor: public MolecularCoor { private: protected: RefSCDimension dim_; // the number of atoms x 3 virtual void init(); public: CartMolecularCoor(Ref<Molecule>&mol); CartMolecularCoor(StateIn&); CartMolecularCoor(const Ref<KeyVal>&); virtual ~CartMolecularCoor(); void save_data_state(StateOut&); virtual RefSCDimension dim(); virtual int to_cartesian(const Ref<Molecule>&,const RefSCVector&internal); virtual int to_internal(RefSCVector&internal); virtual int to_cartesian(RefSCVector&cartesian,RefSCVector&internal); virtual int to_internal(RefSCVector&internal,RefSCVector&cartesian); virtual int to_cartesian(RefSymmSCMatrix&cart,RefSymmSCMatrix&internal); virtual int to_internal(RefSymmSCMatrix&internal,RefSymmSCMatrix&cart); virtual void print(std::ostream& =ExEnv::out0()) const; virtual void print_simples(std::ostream& =ExEnv::out0()) const; void guess_hessian(RefSymmSCMatrix&hessian); RefSymmSCMatrix inverse_hessian(RefSymmSCMatrix&); }; } #endif // Local Variables: // mode: c++ // c-file-style: "CLJ" // End: