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bem.h // // bem.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_solvent_bem_h #define _chemistry_solvent_bem_h #include <util/class/class.h> #include <util/state/state.h> #include <util/keyval/keyval.h> #include <math/isosurf/volume.h> #include <math/isosurf/surf.h> #include <math/scmat/matrix.h> #include <chemistry/molecule/molecule.h> namespace sc { // This represents a solvent by a polarization charge on a dielectric // boundary surface. class BEMSolvent: public DescribedClass { private: int debug_; Ref<Molecule> solute_; Ref<Molecule> solvent_; double solvent_density_; double dielectric_constant_; Ref<SCMatrixKit> matrixkit_; RefSCMatrix system_matrix_i_; double f_; Ref<MessageGrp> grp_; double area_; double volume_; double computed_enclosed_charge_; double edisp_; double erep_; Ref<TriangulatedImplicitSurface> surf_; double** alloc_array(int n, int m); void free_array(double**); // This holds the area associated with each vertex. It is used // to convert charges to charge densities and back. double* vertex_area_; // Given charges compute surface charge density. void charges_to_surface_charge_density(double *charges); // Given surface charge density compute charges. void surface_charge_density_to_charges(double *charges); public: BEMSolvent(const Ref<KeyVal>&); virtual ~BEMSolvent(); // This should be called after everything is setup--the // molecule has the correct the geometry and all of the // parameters have been adjusted. void init(); // This gets rid of the system matrix inverse and, optionally, the surface. void done(int clear_surface = 1); int ncharge() { return surf_->nvertex(); } Ref<Molecule> solvent() { return solvent_ ;} double solvent_density() { return solvent_density_ ;} // NOTE: call allocation routines after init and free routines before done double** alloc_charge_positions() { return alloc_array(ncharge(), 3); } void free_charge_positions(double**a) { free_array(a); } double** alloc_normals() { return alloc_array(ncharge(), 3); } void free_normals(double**a) { free_array(a); } double* alloc_efield_dot_normals() { return new double[ncharge()]; } void free_efield_dot_normals(double*a) { delete[] a; } double* alloc_charges() { return new double[ncharge()]; } void free_charges(double*a) { delete[] a; } void charge_positions(double**); void normals(double**); // Given the efield dotted with the normals at the charge positions this // will compute a new set of charges. void compute_charges(double* efield_dot_normals, double* charge); // Given a set of charges and a total charge, this will normalize // the integrated charge to the charge that would be expected on // the surface if the given total charge were enclosed within it. void normalize_charge(double enclosed_charge, double* charges); // Given charges and nuclear charges compute their interation energy. double nuclear_charge_interaction_energy(double *nuclear_charge, double** charge_positions, double* charge); // Given charges compute the interaction energy between the nuclei // and the point charges. double nuclear_interaction_energy(double** charge_positions, double* charge); // Given charges compute the interaction energy for just the surface. double self_interaction_energy(double** charge_positions, double *charge); // Given the charges, return the total polarization charge on the surface. double polarization_charge(double* charge); // Return the area (available after compute_charges called). double area() const { return area_; } // Return the volume (available after compute_charges called). double volume() const { return volume_; } // Return the enclosed charge (available after compute_charges called). double computed_enclosed_charge() const { return computed_enclosed_charge_; } double disp() {return edisp_;} double rep() {return erep_;} double disprep(); // this never needs to be called explicitly, but is here now for debugging void init_system_matrix(); Ref<TriangulatedImplicitSurface> surface() const { return surf_; } Ref<SCMatrixKit> matrixkit() { return matrixkit_; } }; } #endif // Local Variables: // mode: c++ // c-file-style: "CLJ" // End: