atomgraph_abstracts.h

// -*-c++-*-
#ifndef STORMM_ATOMGRAPH_ABSTRACTS_H
#define STORMM_ATOMGRAPH_ABSTRACTS_H
 
#include "copyright.h"
#include "atomgraph_enumerators.h"
 
namespace stormm {
namespace topology {

template <typename T> struct UreyBradleyTerm {
  int i_atom;     
  int k_atom;     
  int param_idx;  
  T keq;          
  T leq;          
};

template <typename T> struct CharmmImprTerm {
  int i_atom;     
  int j_atom;     
  int k_atom;     
  int l_atom;     
  int param_idx;  
  T keq;          
  T phi_eq;       
};

template <typename T> struct CmapTerm {
  int i_atom;     
  int j_atom;     
  int k_atom;     
  int l_atom;     
  int m_atom;     
  int surf_idx;   
  int surf_dim;   
  T* surf;        
};

template <typename T> struct BondTerm {
  int i_atom;     
  int j_atom;     
  int param_idx;  
  T keq;          
  T leq;          
};

template <typename T> struct AngleTerm {
  int i_atom;     
  int j_atom;     
  int k_atom;     
  int param_idx;  
  T keq;          
  T theta_eq;     
};

template <typename T> struct DihedralTerm {
  int i_atom;     
  int j_atom;     
  int k_atom;     
  int l_atom;     
  int param_idx;  
  T amplitude;    
  T phase;        
  T periodicity;  
  T elec_screen;  
  T vdw_screen;   
};

template <typename T> struct ValenceKit {

  explicit ValenceKit(int natom_in, int nbond_in, int nangl_in, int ndihe_in, int nbond_param_in,
                      int nangl_param_in, int ndihe_param_in, int ninfr14_in, int nattn14_param_in,
                      int nubrd_in, int ncimp_in, int ncmap_in, int nubrd_param_in,
                      int ncimp_param_in, int ncmap_surf_in, const T* bond_keq_in,
                      const T* bond_leq_in, const T* angl_keq_in,
                      const T* angl_theta_in, const T* dihe_amp_in, const T* dihe_freq_in,
                      const T* dihe_phi_in, const T* attn14_elec_in, const T* attn14_vdw_in,
                      const int* bond_i_atoms_in, const int* bond_j_atoms_in,
                      const int* bond_param_idx_in, const char4* bond_modifiers_in,
                      const uint* bond_relevance_in, const int* angl_i_atoms_in,
                      const int* angl_j_atoms_in, const int* angl_k_atoms_in,
                      const int* angl_param_idx_in, const char4* angl_modifiers_in,
                      const uint* angl_relevance_in, const int* dihe_i_atoms_in,
                      const int* dihe_j_atoms_in, const int* dihe_k_atoms_in,
                      const int* dihe_l_atoms_in, const int* dihe_param_idx_in,
                      const int* dihe14_param_idx_in, const char4* dihe_modifiers_in,
                      const int* infr14_i_atoms_in, const int* infr14_l_atoms_in,
                      const int* infr14_param_idx_in, const int* ubrd_i_atoms_in,
                      const int* ubrd_k_atoms_in, const int* ubrd_param_idx_in,
                      const int* cimp_i_atoms_in, const int* cimp_j_atoms_in,
                      const int* cimp_k_atoms_in, const int* cimp_l_atoms_in,
                      const int* cimp_param_idx_in, const int* cmap_i_atoms_in,
                      const int* cmap_j_atoms_in, const int* cmap_k_atoms_in,
                      const int* cmap_l_atoms_in, const int* cmap_m_atoms_in,
                      const int* cmap_dim_in, const int* cmap_surf_bounds_in,
                      const int* cmap_patch_bounds_in, const int* cmap_surf_idx_in,
                      const T* ubrd_keq_in, const T* ubrd_leq_in, const T* cimp_keq_in,
                      const T* cimp_phi_in, const T* cmap_surf_in, const T* cmap_dphi_in,
                      const T* cmap_dpsi_in, const T* cmap_dphi_dpsi_in, const T* cmap_patches_in,
                      const int* bond_asgn_atoms_in, const int* bond_asgn_index_in,
                      const int* bond_asgn_terms_in, const int* bond_asgn_bounds_in,
                      const int* angl_asgn_atoms_in, const int* angl_asgn_index_in,
                      const int* angl_asgn_terms_in, const int* angl_asgn_bounds_in,
                      const int* dihe_asgn_atoms_in, const int* dihe_asgn_index_in,
                      const int* dihe_asgn_terms_in, const int* dihe_asgn_bounds_in,
                      const int* ubrd_asgn_atoms_in, const int* ubrd_asgn_index_in,
                      const int* ubrd_asgn_terms_in, const int* ubrd_asgn_bounds_in,
                      const int* cimp_asgn_atoms_in, const int* cimp_asgn_index_in,
                      const int* cimp_asgn_terms_in, const int* cimp_asgn_bounds_in,
                      const int* cmap_asgn_atoms_in, const int* cmap_asgn_index_in,
                      const int* cmap_asgn_terms_in, const int* cmap_asgn_bounds_in);

  ValenceKit(const ValenceKit &original) = default;
  ValenceKit(ValenceKit &&other) = default;
  
  // The purpose of this struct is to store a collection of pointers for HPC kernels.  As such, it
  // does not have any private member variables.  As a provider of parameters, it also does not
  // allow modification of the data that it points to.
  const int natom;              
  const int nbond;              
  const int nangl;              
  const int ndihe;              
  const int nbond_param;        
  const int nangl_param;        
  const int ndihe_param;        
  const int ninfr14;            
  const int nattn14_param;      
  const int nubrd;              
  const int ncimp;              
  const int ncmap;              
  const int nubrd_param;        
  const int ncimp_param;        
  const int ncmap_surf;         
  const T* bond_keq;            
  const T* bond_leq;            
  const T* angl_keq;            
  const T* angl_theta;          
  const T* dihe_amp;            
  const T* dihe_freq;           
  const T* dihe_phi;            
  const T* attn14_elec;         
  const T* attn14_vdw;          
  const int* bond_i_atoms;      
  const int* bond_j_atoms;      
  const int* bond_param_idx;    
  const char4* bond_modifiers;  
  const uint* bond_relevance;   
  const int* angl_i_atoms;      
  const int* angl_j_atoms;      
  const int* angl_k_atoms;      
  const int* angl_param_idx;    
  const char4* angl_modifiers;  
  const uint* angl_relevance;   
  const int* dihe_i_atoms;      
  const int* dihe_j_atoms;      
  const int* dihe_k_atoms;      
  const int* dihe_l_atoms;      
  const int* dihe_param_idx;    
  const int* dihe14_param_idx;  
  const char4* dihe_modifiers;  
  const int* infr14_i_atoms;    
  const int* infr14_l_atoms;    
  const int* infr14_param_idx;  
  const int* ubrd_i_atoms;      
  const int* ubrd_k_atoms;      
  const int* ubrd_param_idx;    
  const int* cimp_i_atoms;      
  const int* cimp_j_atoms;      
  const int* cimp_k_atoms;      
  const int* cimp_l_atoms;      
  const int* cimp_param_idx;    
  const int* cmap_i_atoms;      
  const int* cmap_j_atoms;      
  const int* cmap_k_atoms;      
  const int* cmap_l_atoms;      
  const int* cmap_m_atoms;      
  const int* cmap_dim;          
  const int* cmap_surf_bounds;  
  const int* cmap_patch_bounds; 
  const int* cmap_surf_idx;     
  const T* ubrd_keq;            
  const T* ubrd_leq;            
  const T* cimp_keq;            
  const T* cimp_phi;            
  const T* cmap_surf;           
  const T* cmap_dphi;           
  const T* cmap_dpsi;           
  const T* cmap_dphi_dpsi;      
  const T* cmap_patches;        
 
  // The following arrays provide a different perspective on the valence terms.  Each bond, angle,
  // dihedral, Urey-Bradley, CMAP, and other valence term is assigned to one of its constituent
  // atoms.  Atoms are then responsible for executing any of their assigned terms.  Atom a_idx
  // is responsible for terms in each array indexed by [(term)_asgn_bounds[a_idx] ...
  // (term)_asgn_bounds[a_idx] + 1), which provides the relevant elements of the associated
  // (term)_asgn_index array (for the parameter index) or the (term)_assigned_atoms array
  // (multiply by (number of atoms in the term - 1), but this lists all other atoms in the term).
  // This allows instant lookup of all relevant bonds, angles, CMAPs, etc. based on any given atom
  // number, although to get all bonds in a given molecule one still has to loop over all atoms in
  // the molecule.  To find all bonds associated with a given atom a_idx, look for all bonds that
  // a_idx itself is responsible for and then cycle through its 1:2 exclusions neighbor list to see
  // which of those atom are responsible for bonds back to a_idx.  That will enumerate all bonds,
  // with parameters, affecting atom a_idx.
  const int* bond_asgn_atoms;  
  const int* bond_asgn_index;  
  const int* bond_asgn_terms;  
  const int* bond_asgn_bounds; 
  const int* angl_asgn_atoms;  
  const int* angl_asgn_index;  
  const int* angl_asgn_terms;  
  const int* angl_asgn_bounds; 
  const int* dihe_asgn_atoms;  
  const int* dihe_asgn_index;  
  const int* dihe_asgn_terms;  
  const int* dihe_asgn_bounds; 
  const int* ubrd_asgn_atoms;  
  const int* ubrd_asgn_index;  
  const int* ubrd_asgn_terms;  
  const int* ubrd_asgn_bounds; 
  const int* cimp_asgn_atoms;  
  const int* cimp_asgn_index;  
  const int* cimp_asgn_terms;  
  const int* cimp_asgn_bounds; 
  const int* cmap_asgn_atoms;  
  const int* cmap_asgn_index;  
  const int* cmap_asgn_terms;  
  const int* cmap_asgn_bounds; 
};

template <typename T> struct NonbondedKit {

  explicit NonbondedKit(int natom_in, int n_q_types_in, int n_lj_types_in,
                        const T coulomb_constant_in, const T* charge_in, const int* q_idx_in,
                        const int* lj_idx_in, const T* q_parameter_in, const T* lja_coeff_in,
                        const T* ljb_coeff_in, const T* ljc_coeff_in, const T* lja_14_coeff_in,
                        const T* ljb_14_coeff_in, const T* ljc_14_coeff_in, const T* lj_sigma,
                        const T* lj_14_sigma, const int* nb11x_in, const int* nb11_bounds_in,
                        const int* nb12x_in, const int* nb12_bounds_in, const int* nb13x_in,
                        const int* nb13_bounds_in, const int* nb14x_in, const int* nb14_bounds_in,
                        const T* lj_type_corr_in);

  NonbondedKit(const NonbondedKit &original) = default;
  NonbondedKit(NonbondedKit &&other) = default;
 
  // Member variables again store a collection of atomic parameters
  const int natom;          
  const int n_q_types;      
  const int n_lj_types;     
  const T coulomb_constant; 
  const T* charge;          
  const int* q_idx;         
  const int* lj_idx;        
  const T* q_parameter;     
  const T* lja_coeff;       
  const T* ljb_coeff;       
  const T* ljc_coeff;       
  const T* lja_14_coeff;    
  const T* ljb_14_coeff;    
  const T* ljc_14_coeff;    
  const T* lj_sigma;        
  const T* lj_14_sigma;     
  const int* nb11x;         
  const int* nb11_bounds;   
  const int* nb12x;         
  const int* nb12_bounds;   
  const int* nb13x;         
  const int* nb13_bounds;   
  const int* nb14x;         
  const int* nb14_bounds;   
  const T* lj_type_corr;    
};

template <typename T> struct ImplicitSolventKit {
 
  explicit ImplicitSolventKit(int natom_in, ImplicitSolventModel igb_in, T dielectric_in,
                              T saltcon_in, const int* neck_gb_idx_in, const T* pb_radii_in,
                              const T* gb_screen_in, const T* gb_alpha_in,
                              const T* gb_beta_in, const T* gb_gamma_in);

  ImplicitSolventKit(const ImplicitSolventKit &original) = default;
  ImplicitSolventKit(ImplicitSolventKit &&other) = default;
 
  // Member variables again store a collection of atomic parameters
  const int natom;                
  const ImplicitSolventModel igb; 
  const T dielectric;             
  const T saltcon;                
  const int* neck_gb_idx;         
  const T* pb_radii;              
  const T* gb_screen;             
  const T* gb_alpha;              
  const T* gb_beta;               
  const T* gb_gamma;              
};

struct ChemicalDetailsKit {

  ChemicalDetailsKit(int natom_in, int nres_in, int nmol_in, int free_dof_in, int cnst_dof_in,
                     const char4* atom_names_in, const char4* res_names_in,
                     const char4* atom_types_in, const int* z_numbers_in, const int* res_limits_in,
                     const int* atom_numbers_in, const int* res_numbers_in, const int* mol_home_in,
                     const int* mol_contents_in, const int* mol_limits_in, const double* masses_in,
                     const float* sp_masses_in, const double* inv_masses_in,
                     const float* sp_inv_masses_in);

  ChemicalDetailsKit(const ChemicalDetailsKit &original) = default;
  ChemicalDetailsKit(ChemicalDetailsKit &&other) = default;
 
  // Member variables store the atom count, residue count, and other ways to quantify the system
  // in addition to many useful pointers
  const int natom;             
  const int nres;              
  const int nmol;              
  const int free_dof;          
  const int cnst_dof;          
  const char4* atom_names;     
  const char4* res_names;      
  const char4* atom_types;     
  const int* z_numbers;        
  const int* res_limits;       
  const int* atom_numbers;     
  const int* res_numbers;      
  const int* mol_home;         
  const int* mol_contents;     
  const int* mol_limits;       
  const double* masses;        
  const float* sp_masses;      
  const double* inv_masses;    
  const float* sp_inv_masses;  
};

template <typename T> struct VirtualSiteKit {

  explicit VirtualSiteKit(int nsite_in, int nframe_set_in, const int* vs_atoms_in,
                          const int* frame1_idx_in, const int* frame2_idx_in,
                          const int* frame3_idx_in, const int* frame4_idx_in,
                          const int* vs_param_idx_in, const int* vs_types_in, const T* dim1_in,
                          const T* dim2_in, const T* dim3_in);

  VirtualSiteKit(const VirtualSiteKit &original) = default;
  VirtualSiteKit(VirtualSiteKit &&other) = default;
 
  const int nsite;          
  const int nframe_set;     
  const int* vs_atoms;      
  const int* frame1_idx;    
  const int* frame2_idx;    
  const int* frame3_idx;    
  const int* frame4_idx;    
  const int* vs_param_idx;  
  const int* vs_types;      
  const T* dim1;            
  const T* dim2;            
  const T* dim3;            
};

template <typename T> struct ConstraintKit {

  explicit ConstraintKit(const int nsettle_in, const int nsett_param_in, const int ngroup_in,
                         const int ncnst_param_in, const int* settle_ox_atoms_in,
                         const int* settle_h1_atoms_in, const int* settle_h2_atoms_in,
                         const int* settle_param_idx_in, const int* group_list_in,
                         const int* group_bounds_in, const int* group_param_idx_in,
                         const int* group_param_bounds_in, const T* settle_mo_in,
                         const T* settle_mh_in, const T* settle_moh_in, const T* settle_mormt_in,
                         const T* settle_mhrmt_in, const T* settle_ra_in, const T* settle_rb_in,
                         const T* settle_rc_in, const T* group_sq_lengths_in,
                         const T* group_inv_masses_in);

  ConstraintKit(const ConstraintKit &original) = default;
  ConstraintKit(ConstraintKit &&other) = default;
  
  const int nsettle;              
  const int nsett_param;          
  const int ngroup;               
  const int ncnst_param;          
  const int* settle_ox_atoms;     
  const int* settle_h1_atoms;     
  const int* settle_h2_atoms;     
  const int* settle_param_idx;    
  const int* group_list;          
  const int* group_bounds;        
  const int* group_param_idx;     
  const int* group_param_bounds;  
  const T* settle_mo;             
  const T* settle_mh;             
  const T* settle_moh;            
  const T* settle_mormt;          
  const T* settle_mhrmt;          
  const T* settle_ra;             
  const T* settle_rb;             
  const T* settle_rc;             
  const T* group_sq_lengths;      
  const T* group_inv_masses;      
};
 
} // namespace topology
} // namespace stormm
 
#include "atomgraph_abstracts.tpp"
 
#endif