findisp.h

//
// findisp.h
//
// Copyright (C) 1997 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_findisp_h
#define _chemistry_molecule_findisp_h
 
#include <iostream>
#include <map>
#include <vector>
#include <algorithm>
 
#include <util/misc/scexception.h>
#include <chemistry/molecule/deriv.h>
#include <chemistry/molecule/energy.h>
 
namespace sc {
 
 
  template <typename Value>
    class Displacements {
      public:
      Displacements() {}
      ~Displacements() {}
 
      void save(StateOut& s) const {
        s.put(disps_);
      }
      void restore(StateIn& s) {
        s.get(disps_);
      }
 
      typedef int Coord;
      typedef double DisplacementSize;
      typedef std::pair<Coord,DisplacementSize> KeyElem;
      typedef std::vector<KeyElem> Key;
      typedef typename std::map< Key, Value>::iterator iter;
      typedef typename std::map< Key, Value>::const_iterator citer;
 
      citer begin() const { return disps_.begin(); }
      citer end() const { return disps_.end(); }
      std::size_t size() const { return disps_.size(); }
 
      std::pair<Key,Value> find(Coord c1, DisplacementSize d1) const {
        Key key;
        key.push_back(std::make_pair(c1,d1));
        return find(key);
      }
      std::pair<Key,Value> find(Coord c1, DisplacementSize d1,
                                Coord c2, DisplacementSize d2) const {
        Key key;
        key.push_back(std::make_pair(c1,d1));
        key.push_back(std::make_pair(c2,d2));
        std::stable_sort(key.begin(), key.end());
        return find(key);
      }
      bool has(const Key& key) const {
        citer v = disps_.find(key);
        return v != disps_.end();
      }
      std::pair<Key,Value> find(const Key& key) const {
        citer v = disps_.find(key);
        if (v == disps_.end())
          throw sc::ProgrammingError("Displacement::find -- displacement not found",__FILE__,__LINE__);
        return *v;
      }
      citer find(const Value& value) const {
        for(citer v = disps_.begin(); v != disps_.end(); ++v) {
          if ((*v).second == value) return v;
        }
        throw sc::ProgrammingError("Displacement::find -- value not found",__FILE__,__LINE__);
      }
 
      void push(Coord c1, DisplacementSize d1,
                const Value& v) {
        Key key;
        key.push_back(std::make_pair(c1,d1));
        return push(key,v);
      }
      void push(Coord c1, DisplacementSize d1,
                Coord c2, DisplacementSize d2,
                const Value& v) {
        Key key;
        key.push_back(std::make_pair(c1,d1));
        key.push_back(std::make_pair(c2,d2));
        std::stable_sort(key.begin(), key.end());
        return push(key,v);
      }
      void push(const Key& key, const Value& v) {
        iter i = disps_.find(key);
        if (i != disps_.end())
          throw sc::ProgrammingError("Displacement::push -- displacement already exists",__FILE__,__LINE__);
        disps_[key] = v;
      }
 
      private:
      std::map< Key, Value> disps_;
  };
 
#if 0
 
  template <unsigned int TargetOrder, typename Function>
  class FinDispDerivative : virtual public SavableState {
    public:
      FinDispDerivative(const Ref<Function>& function);
      FinDispDerivative(StateIn&);
      ~FinDispDerivative();
      void save_data_state(StateOut&);
 
      typedef typename Function::Value FunctionValue;
      typedef typename Function::Parameter FunctionParameter;
      static const unsigned int TensorTraits<FunctionParameter>::rank param_rank;
      const ParameterDerivative<FunctionValue,IntegerProduct<TargetOrder,param_rank>::value>::result Result;
 
      const Result& result();
    private:
      static ClassDesc class_desc_;
      Ref<Function> function_;
      Result result_;
 
      void compute();
  };
#endif
 
  struct EGH {
    public:
      EGH();
      EGH(double e, const RefSCVector& g, const RefSymmSCMatrix& h);
      ~EGH();
 
      double energy() const { return energy_; }
      const RefSCVector& gradient() const { return gradient_; }
      const RefSymmSCMatrix& hessian() const { return hessian_; }
 
    private:
      double energy_;
      RefSCVector gradient_;
      RefSymmSCMatrix hessian_;
  };
  template <> void FromStateIn<EGH>(EGH& v, StateIn& s, int& count);
  template <> void ToStateOut<EGH>(const EGH& v, StateOut& so, int& count);
 
 
class FinDispMolecularHessian: public MolecularHessian {
 
  class Params : virtual public SavableState {
    public:
      Params();
      Params(const Ref<KeyVal>& kv);
      Params(StateIn&);
      ~Params();
      void save_data_state(StateOut&);
 
      const Ref<PointGroup>& disp_pg() const { return disp_pg_; }
      double disp_size() const { return disp_; }
      bool only_totally_symmetric() const { return only_totally_symmetric_; }
      bool user_provided_eliminate_quadratic_terms() const { return user_provided_eliminate_quadratic_terms_; }
      bool eliminate_quadratic_terms() const { return eliminate_quadratic_terms_; }
      bool do_null_displacement() const { return do_null_displacement_; }
      int debug() const { return debug_; }
      bool checkpoint() const { return checkpoint_; }
      const std::string& checkpoint_file() const { return checkpoint_file_; }
      bool restart() const { return restart_; }
      const std::string& restart_file() const { return restart_file_; }
      bool use_energies() const { return use_energies_; }
      double gradient_accuracy() const { return gradient_accuracy_; }
      double energy_accuracy() const { return energy_accuracy_; }
      int nirrep() const { return disp_pg_->char_table().nirrep(); }
 
      // if called will no need to (re)compute default
      void set_eliminate_quadratic_terms(bool e) {
        user_provided_eliminate_quadratic_terms_ = true;
        eliminate_quadratic_terms_ = e;
      }
      void set_disp_size(double s);
      void set_disp_pg(const Ref<PointGroup>& pg) { disp_pg_ = pg; }
      void set_restart(bool r = true) { restart_ = r; }
      void set_checkpoint(bool c = true) { checkpoint_ = c; }
      void set_desired_accuracy(double acc);
 
    private:
      static ClassDesc class_desc_;
 
      // In case molecule must be given in lower symmetry, its actual
      // symmetry and the symmetry used to compute displacements is this
      Ref<PointGroup> disp_pg_;
      // the cartesian displacement size in bohr
      double disp_;
      // only do the totally symmetric displacements (makes sense if the Hessian is to be used in geometry optimization)
      bool only_totally_symmetric_;
      // eliminate the quadratic terms in the hessian by doing an extra displacement for
      // each of the totally-symmetric coordinates
      bool eliminate_quadratic_terms_;
      bool user_provided_eliminate_quadratic_terms_; // whether user provided the value eliminate_quadratic_terms
                                                     // if true, will skip the MolecularEnergy-dependent default override
      // use the gradient at the initial geometry to remove first order terms
      // (important if not at equilibrium geometry)
      bool do_null_displacement_;
      // print flag
      int debug_;
      // whether or not to checkpoint
      bool checkpoint_;
      // the name of the checkpoint file
      std::string checkpoint_file_;
      // whether or not to attempt a restart
      bool restart_;
      // the name of the restart file
      std::string restart_file_;
      // force computation from energies
      bool use_energies_;
      // the accuracy for energy calculations
      double energy_accuracy_;
      // the accuracy for gradient calculations
      double gradient_accuracy_;
  };
 
 
    // Implements FinDispMolecularHessian
    class Impl : virtual public SavableState {
      public:
      typedef Displacements<EGH>::Key Displacement;
 
      Impl(const Ref<MolecularEnergy>& e,
           const Ref<Params>& params);
      Impl(StateIn& s);
      ~Impl();
      void save_data_state(StateOut& s);
 
      void checkpoint_displacements(StateOut&);
      void restore_displacements(StateIn&);
 
      const Ref<Params>& params() const { return params_; }
      const Ref<MolecularEnergy>& mole() const { return mole_; }
      void set_mole(const Ref<MolecularEnergy>& mole) { mole_ = mole; }
      virtual int ndisplace() const =0;
      // returns a matrix whose columns are SALC displacements
      RefSCMatrix displacements(int irrep) const;
      void displace(const Displacement& d);
      void original_geometry();
 
      virtual void init();
      virtual void restart();
 
      RefSymmSCMatrix cartesian_hessian();
 
      // transforms hessian in symmetrized coordinates to cartesian coordinates
      void do_hess_for_irrep(int irrep,
                             const RefSymmSCMatrix &dhessian,
                             const RefSymmSCMatrix &xhessian);
 
      protected:
      Ref<Params> params_;
 
      Ref<MolecularEnergy> mole_;
      // The molecule's original point group for restoration at the end.
      Ref<PointGroup> original_point_group_;
      // The molecule's original geometry for restoration at the end and
      //computing displacements.
      RefSCVector original_geometry_;
      // a basis for the symmetrized cartesian coordinates (rows)
      RefSCMatrix symbasis_;
 
      // values, gradients, and hessians at various (displaced) geometries
      Displacements<EGH> values_;
 
      virtual RefSymmSCMatrix compute_hessian() =0;
      virtual void compute_mole(const Displacement& d) =0;
 
      Ref<SCMatrixKit> matrixkit() const { return mole_->matrixkit(); }
      RefSCDimension d3natom() const { return mole_->moldim(); }
      unsigned int coor_to_irrep(unsigned int symm_coord) const;
 
      static ClassDesc class_desc_;
    };
 
    // Implementation of finite-difference hessians from gradients
    class GradientsImpl : public Impl {
      public:
        GradientsImpl(const Ref<MolecularEnergy>& e,
                      const Ref<Params>& params);
        GradientsImpl(StateIn& s);
        ~GradientsImpl();
        void save_data_state(StateOut& s);
 
      private:
 
        // will throw if mole lacks gradients capability; do nothing if mole is null
        static void validate_mole(const Ref<MolecularEnergy>& e);
        int ndisplace() const;
        void set_gradient(const Displacement& d, double energy, const RefSCVector &grad);
        RefSymmSCMatrix compute_hessian();
        void compute_mole(const Displacement& d);
 
        static ClassDesc class_desc_;
    };
 
    // Implementation of finite-difference hessians from energies
    class EnergiesImpl : public Impl {
      public:
        // will throw if mole lacks energies capability; do nothing if mole is null
        EnergiesImpl(const Ref<MolecularEnergy>& e,
                     const Ref<Params>& params);
        EnergiesImpl(StateIn& s);
        ~EnergiesImpl();
        void save_data_state(StateOut& s);
 
      private:
 
        static void validate_mole(const Ref<MolecularEnergy>& e);
        int ndisplace() const;
        RefSymmSCMatrix compute_hessian();
        void compute_mole(const Displacement& d);
        const Displacements<EGH>& values() const { return values_; }
 
        struct Eij {
            Eij(int i, int j, EnergiesImpl& eimpl) :
              i_(i), j_(j), eimpl_(eimpl)
            {
            }
 
            // return energy computed at geometry displaced by di (in units of disp_)
            // along i and dj along j
            double operator()(int di, int dj) {
              Displacement disp;
              if (i_ != j_) {
                if (di != 0) disp.push_back(std::make_pair(i_,double(di)));
                if (dj != 0) disp.push_back(std::make_pair(j_,double(dj)));
              }
              else { // i_ == j_
                if (di+dj != 0) disp.push_back(std::make_pair(i_,double(di+dj)));
              }
              eimpl_.compute_mole(disp);
              const double energy = eimpl_.values().find(disp).second.energy();
              return energy;
            }
 
            int i_, j_;
            EnergiesImpl& eimpl_;
        };
 
        static ClassDesc class_desc_;
    };
 
  private:
    Ref<Impl> pimpl_; //<< initliazed lazily
    Ref<MolecularEnergy> mole_init_;   //< pimpl_ is initalized lazily, so this is used to hold the MolecularEnergy object used to initialize the pimpl_
    Ref<Params> params_;
 
    void override_default_params(); // override some defaults based on the properties of MolecularEnergy
 
  protected:
 
    void init_pimpl(const Ref<MolecularEnergy>& e);
    void restart();
 
  public:
    FinDispMolecularHessian(const Ref<MolecularEnergy>&);
    FinDispMolecularHessian(const Ref<KeyVal>&);
    FinDispMolecularHessian(StateIn&);
    ~FinDispMolecularHessian();
    void save_data_state(StateOut&);
 
    RefSymmSCMatrix cartesian_hessian();
 
    void set_energy(const Ref<MolecularEnergy> &energy);
    MolecularEnergy* energy() const { return pimpl_ ? pimpl_->mole().pointer() : 0; }
 
    const Ref<Params>& params() const { return params_; }
 
    void set_desired_accuracy(double acc);
};
 
class FinDispMolecularGradient: public MolecularGradient {
//
//  public:
//
//    class Displacements {
//      public:
//
//      private:
//        /** displacements are represented as a key -> index map
//         *  keys are formatted as comma-separated list of integer,double pairs
//         *  each pair contains the index of SALC (0-based) + displacement size
//         *  SALC indices are nondecreasing
//         */
//        std::map< std::list< std::pair<int,double> >, > disps;
//    };
 
  protected:
    Ref<MolecularEnergy> mole_;
    // In case molecule must be given in lower symmetry, its actual
    // symmetry and the symmetry used to compute displacements is this
    Ref<PointGroup> displacement_point_group_;
    // The molecule's original geometry for restoration at the end and
    //computing displacements.
    RefSCVector original_geometry_;
    // the cartesian displacement size in bohr
    double disp_;
    // the accuracy of the energy computations
    double energy_accuracy_;
    // whether or not to attempt a restart
    int restart_;
    // the name of the restart file
    std::string restart_file_;
    // whether or not to checkpoint
    int checkpoint_;
    // the name of the checkpoint file
    std::string checkpoint_file_;
    // 2-pt formula for gradient is accurate to O(h^2) (contaminated by 3rd derivatives)
    // make it O(h^4), i.e. eliminate the h^2 terms, by using a 4-pt formula
    int eliminate_quadratic_terms_;
    // print flag
    int debug_;
    // a basis for the symmetrized cartesian coordinates
    RefSCMatrix symbasis_;
    // the energies at each of the completed displacements
    std::vector<double> energies_;
 
    // given displacement # disp returns internal coordinate index and displacement size (in units of disp_)
    void get_disp(int disp, int &index, double &dispsize);
//    void do_grad_for_irrep(int irrep,
//                           const RefSymmSCMatrix &dhessian,
//                           const RefSymmSCMatrix &xhessian);
    void init();
    void restart();
 
    RefSCVector compute_gradient();
    int ndisplace() const;
    int ndisplacements_done() const { return energies_.size(); }
    RefSCMatrix displacements(int irrep) const;
    void displace(int disp);
    void original_geometry();
    //void set_gradient(int disp, const RefSCVector &grad);
    void checkpoint_displacements(StateOut&);
    void restore_displacements(StateIn&);
 
  public:
    FinDispMolecularGradient(const Ref<MolecularEnergy>&);
    FinDispMolecularGradient(const Ref<KeyVal>&);
    FinDispMolecularGradient(StateIn&);
    ~FinDispMolecularGradient();
    void save_data_state(StateOut&);
 
 
    RefSCVector cartesian_gradient();
 
    void set_checkpoint(int c) { checkpoint_ = c; }
    int checkpoint() const { return checkpoint_; }
 
    void set_energy(const Ref<MolecularEnergy> &energy);
    MolecularEnergy* energy() const;
 
    Ref<SCMatrixKit> matrixkit() const { return mole_->matrixkit(); }
    RefSCDimension d3natom() const { return mole_->moldim(); }
 
    void set_desired_accuracy(double acc);
 
    void set_eliminate_quadratic_terms(bool e) { eliminate_quadratic_terms_ = e; }
    void set_disp_size(double s);
};
 
// end of addtogroup ChemistryMolecule
 
}
 
#endif
 
// Local Variables:
// mode: c++
// c-file-style: "CLJ"
// End: