Parameters.h

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/*
   The Parameters class is used to read in and store all of the parameters
   from the parameter files.  These parameters are stored and used to assign
   constants to bonds and atoms as they are read in from the psf file
*/

#ifndef PARAM_H

#define PARAM_H

#include "parm.h"

#include "ReadAmberParm.h"

#include "common.h"
#include "structures.h"
#include "strlib.h"
#include "MStream.h"
//****** BEGIN CHARMM/XPLOR type changes
#include "SimParameters.h"
//****** END CHARMM/XPLOR type changes

#include "GromacsTopFile.h"
#define ACCELERATED_INPUT 1
#ifdef ACCELERATED_INPUT
#include "TupleString.h"
#define ACCELERATED_INPUT_ANGLES 1
#define ACCELERATED_INPUT_DIHEDRALS 1
#define ACCELERATED_INPUT_IMPROPERS 1
#define ACCELERATED_INPUT_CROSSTERMS 1
#define ACCELERATED_INPUT_VDW 1
#define ACCELERATED_INPUT_NBTHOLE 1
#define ACCELERATED_INPUT_TABLE_PAIR 1
#if defined(ACCELERATED_INPUT_NBTHOLE) && ! defined(ACCELERATED_INPUT_VDW)
static_assert(false, "ACCELERATED_INPUT_NBTHOLE requires ACCELERATED_INPUT_VDW");
#endif

#if defined(ACCELERATED_INPUT_TABLE_PAIR) && ! defined(ACCELERATED_INPUT_VDW)
static_assert(false, "ACCELERATED_INPUT_TABLE_PAIR requires ACCELERATED_INPUT_VDW");
#endif
#endif // ACCELERATED_INPUT

class Communicate;
class StringList;

//  The class Parameters is used to store and query the parameters for
//  bonds and atoms.  If the Parameter object resides on the master
//  process, it is responsible for reading in all the parameters and
//  then communicating them to the other processors.  To do this, first
//  the routine read_paramter_file is called to read in each parameter
//  file.  The information that is read in is stored in binary trees
//  for vdw, bond, and angle information and in linked lists for 
//  dihedrals and impropers.  Once all of the files have been read
//  in, the routine done_reading_files is called.  At this point, all
//  of the data that has been read in is copied to arrays.  This is
//  so that each bond and atom can be assigned an index into these
//  arrays to retreive the parameters in constant time.
//
//  Then the psf file is read in.  Each bond and atom is assigned an
//  index into the parameter lists using the functions assign_*_index.
//  Once the psf file has been read in, then the routine 
//  done_reading_structre is called to tell the object that it no
//  longer needs to store the binary trees and linked lists that were
//  used to query the parameters based on atom type.  From this point
//  on, only the indexes will be used.
//
//  The master node then uses send_parameters to send all of these
//  parameters to the other nodes and the objects on all of the other
//  nodes use receive_parameters to accept these parameters.
//
//  From this point on, all of the parameter data is static and the
//  functions get_*_params are used to retrieve the parameter data
//  that is desired.

//  Define the number of Multiples that a Dihedral or Improper
//  bond can have with the Charm22 parameter set
#define MAX_MULTIPLICITY        6

//  Number of characters maximum allowed for storing atom type names
#define MAX_ATOMTYPE_CHARS      6

//****** BEGIN CHARMM/XPLOR type changes
//  Define the numbers associated with each possible parameter-file 
//  type (format) NAMD can handle.
#define paraXplor               0
#define paraCharmm              1
//****** END CHARMM/XPLOR type changes

class Molecule;

class BondValue {
public:
  BondValue() : k(0), x0(0), x1(0) { }
  Real k;    //  Force constant for the bond
  Real x0;   //  Rest distance for the bond
  Real x1;   //  Upper wall for harmonic wall potential (with x0 lower wall)
};

class AngleValue {
public:
        Real k;         //  Force constant for angle
        Real theta0;    //  Rest angle for angle
        Real k_ub;      //  Urey-Bradley force constant
        Real r_ub;      //  Urey-Bradley distance
  int normal; // Whether we use harmonic (1) or cos-based (0) angle terms
};

typedef struct four_body_consts
{
        Real k;         //  Force constant
        int n;          //  Periodicity
        Real delta;     //  Phase shift
} FourBodyConsts;

class DihedralValue {
public:
        int multiplicity;
        FourBodyConsts values[MAX_MULTIPLICITY];
};

class ImproperValue {
public:
        int multiplicity;
        FourBodyConsts values[MAX_MULTIPLICITY];
};

struct CrosstermData { BigReal d00,d01,d10,d11; };

class CrosstermValue {
public:
#ifdef ACCELERATED_INPUT  
        int dimension;
#endif  
        enum {dim=25};
        CrosstermData c[dim][dim];  // bicubic interpolation coefficients
};

// JLai
class GromacsPairValue {
public:
    BigReal pairC6;
    BigReal pairC12;
/*    BigReal A;
    BigReal B;
    BigReal A14;
    BigReal B14;
    BigReal sqrt26;
    BigReal expo;*/
};
// End of JLai


class NonbondedExclValue {
public:
        // need to put parameters here...
        // for now, copy bond
        Real k;         //  Force constant for the bond
        Real x0;        //  Rest distance for the bond
};

typedef struct vdw_val
{
        Real sigma;     //  Sigma value
        Real epsilon;   //  Epsilon value
        Real sigma14;   //  Sigma value for 1-4 interactions
        Real epsilon14; //  Epsilon value for 1-4 interactions
} VdwValue;

//  IndexedVdwPair is used to form a binary search tree that is
//  indexed by vwd_type index.  This is the tree that will be
//  used to search during the actual simulation

typedef struct indexed_vdw_pair
{
        Index ind1;             //  Index for first atom type
        Index ind2;             //  Index for second atom type
        Real A;                 //  Parameter A for this pair
        Real A14;               //  Parameter A for 1-4 interactions
        Real B;                 //  Parameter B for this pair
        Real B14;               //  Parameter B for 1-4 interactions
        struct indexed_vdw_pair *right;  //  Right child
        struct indexed_vdw_pair *left;   //  Left child
} IndexedVdwPair;

#ifdef ACCELERATED_INPUT_VDW
typedef struct indexed_vdw_pair_accel
{
        Index ind1;             //  Index for first atom type
        Index ind2;             //  Index for second atom type
        Real A;                 //  Parameter A for this pair
        Real A14;               //  Parameter A for 1-4 interactions
        Real B;                 //  Parameter B for this pair
        Real B14;               //  Parameter B for 1-4 interactions
  inline indexed_vdw_pair_accel(Index _ind1, Index _ind2, Real _A, Real _A14, Real _B, Real _B14):
    ind1(_ind1), ind2(_ind2), A(_A), A14(_A14), B(_B), B14(_B14){}
  inline indexed_vdw_pair_accel(){}
} IndexedVdwPairAccel;
#endif

typedef struct indexed_nbthole_pair
{
        Index ind1;             //  Index for first atom type
        Index ind2;             //  Index for second atom type
        Real alphai;           //  Parameter alpha for this pair
        Real alphaj;           //  Parameter alpha for this pair
        Real tholeij;          //  Parameter thole for this pair
        struct indexed_nbthole_pair *right;  //  Right child
        struct indexed_nbthole_pair *left;   //  Left child
} IndexedNbtholePair;

typedef struct nbthole_pair_value
{
        Index ind1;             //  Index for first atom type
        Index ind2;             //  Index for second atom type
        Real alphai;           //  Parameter alpha for this pair
        Real alphaj;           //  Parameter alpha for this pair
        Real tholeij;          //  Parameter thole for this pair
  inline nbthole_pair_value(Index _ind1, Index _ind2, Real _tholeij) : ind1(_ind1), ind2(_ind2), tholeij(_tholeij){};
  inline nbthole_pair_value(){}
  // we don't initialize alpha[ij], they are unused

} NbtholePairValue;

//  IndexedTablePair is used to form a binary search tree that is
//  indexed by table_type index.  This is the tree that will be
//  used to search during the actual simulation

typedef struct indexed_table_pair
{

        Index ind1;             //  Index for first atom type
        Index ind2;             //  Index for second atom type
        int K;                  //  number of the table type for this pair
#ifndef ACCELERATED_INPUT_TABLE_PAIR  
        struct indexed_table_pair *right;        //  Right child
        struct indexed_table_pair *left;         //  Left child
#else
  inline indexed_table_pair(Index _ind1, Index _ind2, int _K) : ind1(_ind1), ind2(_ind2), K(_K){};
  inline indexed_table_pair(){}

#endif
} IndexedTablePair;

//  Structures that are defined in Parameters.C
struct bond_params;
struct angle_params;
struct improper_params;
struct dihedral_params;
struct crossterm_params;
struct vdw_params;
struct vdw_pair_params;
struct nbthole_pair_params;
struct table_pair_params;

class Parameters
{
private:
        void initialize();                      //  zeros out pointers

        char *atomTypeNames;                    //  Names of atom types
        Bool AllFilesRead;                      //  Flag TRUE imples that all
                                                //  of the parameter files
                                                //  have been read in and
                                                //  the arrays have been
                                                //  created.
//****** BEGIN CHARMM/XPLOR type changes
        int paramType;                          //  Type (format) of parameter-file
//****** END CHARMM/XPLOR type changes
        bool cosAngles; // True if some angles may be cos-based
        struct bond_params *bondp;              //  Binary tree of bond params
        bool strictSort; // mem_opt requires alpha order sorting
#ifdef ACCELERATED_INPUT
        TwoLevelParam <2, BondValue> *bondmap;  //  Unordered map and vector of bond params
        TwoLevelParam <3, AngleValue> *anglemap;        //  Unordered map and vector of angle params
        TwoLevelParam <4, DihedralValue> *dihedralmap;  //  Unordered map and vector of dihedral params
        TupleString4 lastDihedralKey;    
        TwoLevelParam <4, ImproperValue> *impropermap;  //  Unordered map and vector of improper params
        TwoLevelParam <8, CrosstermValue> *crosstermmap;        //  Unordered map and vector of crossterm params
        TwoLevelParam <1, VdwValue> *vdwmap;    //  Unordered map and vector of Vdw params
#ifdef ACCELERATED_INPUT_VDW
  // for these we don't even need to keep string keyed data structures
  // so we go straight to maps
        std::unordered_map <uint64_t, IndexedVdwPairAccel> vdwpairmap;  //  Unordered map of vdw index pairs
#ifdef ACCELERATED_INPUT_NBTHOLE
        std::unordered_map <uint64_t, NbtholePairValue> nbtholepairmap; //  Unordered map of nbthole index pairs
#endif
#ifdef ACCELERATED_INPUT_TABLE_PAIR
        std::unordered_map <uint64_t, IndexedTablePair> tablepairmap;   //  Unordered map of table index pairs
#endif
  
#endif
#endif
        struct angle_params *anglep;            //  Binary tree of angle params
        struct improper_params *improperp;      //  Linked list of improper par.
        struct dihedral_params *dihedralp;      //  Linked list of dihedral par.
        struct crossterm_params *crosstermp;    //  Linked list of cross-term par.
        struct vdw_params *vdwp;                //  Binary tree of vdw params
        struct vdw_pair_params *vdw_pairp;      //  Binary tree of vdw pairs
        struct nbthole_pair_params *nbthole_pairp;      //  Binary tree of nbthole pairs
        struct table_pair_params *table_pairp;  //  Binary tree of table pairs
public:
        BondValue *bond_array;                  //  Array of bond params
        AngleValue *angle_array;                //  Array of angle params
        DihedralValue *dihedral_array;          //  Array of dihedral params
        ImproperValue *improper_array;          //  Array of improper params
        CrosstermValue *crossterm_array;        //  Array of crossterm params
        // JLai
        GromacsPairValue *gromacsPair_array;    //  Array of gromacsPair params
        // End of JLai
        VdwValue *vdw_array;                    //  Array of vdw params
        NbtholePairValue *nbthole_array;        //  Array of nbthole params
        int numenerentries;                     //  Number of entries for enertable
        int rowsize;
        int columnsize;
        BigReal* table_ener;                    //  Table for tabulated energies
        IndexedVdwPair *vdw_pair_tree;          //  Tree of vdw pair params
        IndexedNbtholePair *nbthole_pair_tree;      //  Tree of nbthole pair params
        IndexedTablePair *tab_pair_tree;                //  Tree of vdw pair params
  int tablenumtypes;
        int NumBondParams;                      //  Number of bond parameters
        int NumAngleParams;                     //  Number of angle parameters
  int NumCosAngles;       // Number of cosine-based angles
        int NumDihedralParams;                  //  Number of dihedral params
        int NumImproperParams;                  //  Number of improper params
        int NumCrosstermParams;                 //  Number of cross-term params
        // JLai
        int NumGromacsPairParams;               //  Number of gromacsPair params
        // End of JLai
        int NumVdwParams;                       //  Number of vdw parameters
        int NumTableParams;                     //  Number of table parameters
  int NumVdwParamsAssigned;               //  Number actually assigned
        int NumVdwPairParams;                   //  Number of vdw_pair params
        int NumNbtholePairParams;                   //  Number of nbthole_pair params
        int NumTablePairParams;                 //  Number of vdw_pair params
        friend class Molecule;
private:
        ResizeArray<char *> error_msgs;         //  Avoids repeating warnings

        int *maxDihedralMults;                  //  Max multiplicity for
                                                //  dihedral bonds
        int *maxImproperMults;                  //  Max multiplicity for
                                                //  improper bonds

        void skip_stream_read(char *, FILE *);  // skip part of stream file

        void add_bond_param(const char *, Bool);//  Add a bond parameter
        struct bond_params *add_to_bond_tree(struct bond_params * , 
                                     struct bond_params *, Bool overwrite);

        void add_angle_param(char *);           //  Add an angle parameter
        struct angle_params *add_to_angle_tree(struct angle_params * , 
                                     struct angle_params *);

        void add_dihedral_param(char *, FILE *); //  Add a dihedral parameter
        void add_to_dihedral_list(struct dihedral_params *);
        void add_to_charmm_dihedral_list(struct dihedral_params *);

        void add_improper_param(char *, FILE *); //  Add an improper parameter
        void add_to_improper_list(struct improper_params *);

        void add_crossterm_param(char *, FILE *); //  Add an cross-term parameter
        void add_to_crossterm_list(struct crossterm_params *);

        void add_vdw_param(char *);             //  Add a vdw parameter
        struct vdw_params *add_to_vdw_tree(struct vdw_params *, 
                                     struct vdw_params *);

        void add_vdw_pair_param(char *);        //  Add a vdw pair parameter
        void add_nbthole_pair_param(char *);        //  Add a nbthole pair parameter        
        void add_table_pair_param(char *);      //  Add a table pair parameter
        void add_to_vdw_pair_list(struct vdw_pair_params *);
        void add_to_nbthole_pair_list(struct nbthole_pair_params *);
        void add_to_table_pair_list(struct table_pair_params *);

        void add_hb_pair_param(char *); //  Add a hydrogen bond pair parameter

        //  All of the traverse routines are used for debugging purposes
        //  to print out the appropriate list of parameters
        void traverse_vdw_pair_params(struct vdw_pair_params *);
        void traverse_nbthole_pair_params(struct nbthole_pair_params *);
        void traverse_vdw_params(struct vdw_params *);
        void traverse_dihedral_params(struct dihedral_params *);
        void traverse_improper_params(struct improper_params *);
        void traverse_crossterm_params(struct crossterm_params *);
        void traverse_angle_params(struct angle_params *);
        void traverse_bond_params(struct bond_params *);

        //  The index_* routines are used to index each of 
        //  the parameters and build the arrays that will be used
        //  for constant time access
        Index index_bonds(struct bond_params *, Index);
        Index index_angles(struct angle_params *, Index);
        Index index_vdw(struct vdw_params *, Index);
        void index_dihedrals();
        void index_impropers();
        void index_crossterms();
        
        void convert_vdw_pairs();
        void convert_nbthole_pairs();
        void convert_table_pairs();
        IndexedVdwPair *add_to_indexed_vdw_pairs(IndexedVdwPair *, IndexedVdwPair *);
        IndexedNbtholePair *add_to_indexed_nbthole_pairs(IndexedNbtholePair *, IndexedNbtholePair *);
        IndexedTablePair *add_to_indexed_table_pairs(IndexedTablePair *, IndexedTablePair *);
        
        int vdw_pair_to_arrays(int *, int *, Real *, Real *, Real *, Real *, 
                               int, IndexedVdwPair *);

        int nbthole_pair_to_arrays(int *, int *, Real *, Real *, Real *, int, IndexedNbtholePair *);
        
        int table_pair_to_arrays(int *, int *, int *, int, IndexedTablePair *);

        //  The free_* routines are used by the destructor to deallocate
        //  memory
        void free_bond_tree(struct bond_params *);
        void free_angle_tree(struct angle_params *);
        void free_dihedral_list(struct dihedral_params *);
        void free_improper_list(struct improper_params *);
        void free_crossterm_list(struct crossterm_params *);
        void free_vdw_tree(struct vdw_params *);
        void free_vdw_pair_tree(IndexedVdwPair *);
        void free_nbthole_pair_tree(IndexedNbtholePair *);
        void free_table_pair_tree(IndexedTablePair *);
        void free_vdw_pair_list();
        void free_nbthole_pair_list(); 

  BigReal interp_lin(BigReal, BigReal, BigReal, BigReal, BigReal); // Perform a linear interpolation for energy table 

        /* does the actual initialization, once the variables have all
           been given default values.  See Parameters() below */
        void read_parm(const GromacsTopFile *, Bool min);
public:
        //****** BEGIN CHARMM/XPLOR type changes
        Parameters();
        Parameters(SimParameters *, StringList *f);
        //****** END CHARMM/XPLOR type changes
        
        Parameters(Ambertoppar *, BigReal);
        void read_parm(Ambertoppar *, BigReal);

        Parameters(AmberParm7Reader::Ambertoppar *, BigReal);
        void read_parm(AmberParm7Reader::Ambertoppar *, BigReal);
        /* initializes this to hold the set of parameters in the
           GROMACS topology file <gf>.  If the parameter <min> is on,
           this assumes that we are going to do minimization and
           therefore can't have atoms with zero VDW - it will add a
           small repulsive term to these. */
        Parameters(const GromacsTopFile *gf, Bool min);
        
        ~Parameters();                          //  Destructor

        // return a string for the Nth atom type.  This can only be
        // called after all the param files have been read and the type
        // names have been indexed.  The Nth atom type refers to the same
        // index of the Nth vdw parameter (i.e. there are NumVdwParams names).
        char *atom_type_name(Index a) {
          return (atomTypeNames + (a * (MAX_ATOMTYPE_CHARS + 1)));
        }
        std::string atom_type_name_str(Index a) const;

        //  Read a parameter file
        void read_parameter_file(char *);

        //****** BEGIN CHARMM/XPLOR type changes
        void read_charmm_parameter_file(char *);
        //****** END CHARMM/XPLOR type changes

        //  Signal the parameter object that all of
        //  the parameter files have been read in
        void done_reading_files(const bool addDrudeBond);

        //  Signal the parameter object that the
        //  structure file has been read in
        void done_reading_structure();
    
        //  The assign_*_index routines are used to assign
        //  an index to atoms or bonds.  If an specific atom
        //  or bond type can't be found, then the program 
        //  terminates
    #ifdef MEM_OPT_VERSION
    void assign_vdw_index(const char *, AtomCstInfo *);
    #else
        void assign_vdw_index(const char *, Atom *);    //  Assign a vdw index to
    #endif
                                                //  an atom
        void assign_bond_index(const char *, const char *, Bond *, bool* bond_found = nullptr);
                                                //  Assign a bond index
                                                //  to a bond
        void assign_angle_index(const char *, const char *, const char *, Angle *, int);
                                                //  Assign an angle index
                                                //  to an angle
        void assign_dihedral_index(const char *, const char*, const char*, const char *, Dihedral *, int, int);
                                                //  Assign a dihedral index
                                                //  to a dihedral
        void assign_improper_index(const char *, const char*, const char*, const char *, Improper *, int);
                                                //  Assign an improper index
                                                //  to an improper
        void assign_crossterm_index(const char *, const char*, const char*, const char *, const char *, const char*, const char*, const char *, Crossterm *);

        //  send_parameters is used by the master process to
        //  communicate the paramters to all the other processors
        void send_Parameters(MOStream *);

        //  receive_parameters is used by all the child processes
        //  to receive the parameters from the master process
        void receive_Parameters(MIStream *);

        //  The get_*_params routines are the routines that really
        //  do all the work for this object.  Given an index, they
        //  access the parameters and return the relevant information
        void get_bond_params(Real *k, Real *x0, Index index)
        {
                *k = bond_array[index].k;
                *x0 = bond_array[index].x0;
        }

        void get_angle_params(Real *k, Real *theta0, Real *k_ub, Real *r_ub,
                              Index index)
        {
                *k = angle_array[index].k;
                *theta0 = angle_array[index].theta0;
                *k_ub = angle_array[index].k_ub;
                *r_ub = angle_array[index].r_ub;
        }

        int get_improper_multiplicity(Index index)
        {
                return(improper_array[index].multiplicity);
        }

        int get_dihedral_multiplicity(Index index)
        {
                return(dihedral_array[index].multiplicity);
        }

        void get_improper_params(Real *k, int *n, Real *delta, 
                                 Index index, int mult)
        {
                if ( (mult<0) || (mult>MAX_MULTIPLICITY) )
                {
                        NAMD_die("Bad mult index in Parameters::get_improper_params");
                }

                *k = improper_array[index].values[mult].k;
                *n = improper_array[index].values[mult].n;
                *delta = improper_array[index].values[mult].delta;
        }

        void get_dihedral_params(Real *k, int *n, Real *delta, 
                                 Index index, int mult)
        {
                if ( (mult<0) || (mult>MAX_MULTIPLICITY) )
                {
                        NAMD_die("Bad mult index in Parameters::get_dihedral_params");
                }

                *k = dihedral_array[index].values[mult].k;
                *n = dihedral_array[index].values[mult].n;
                *delta = dihedral_array[index].values[mult].delta;
        }

        void get_vdw_params(Real *sigma, Real *epsilon, Real *sigma14, 
                            Real *epsilon14, Index index)
  {
    if ( vdw_array ) {
      *sigma = vdw_array[index].sigma;
      *epsilon = vdw_array[index].epsilon;
      *sigma14 = vdw_array[index].sigma14;
      *epsilon14 = vdw_array[index].epsilon14;
    } else {
      // sigma and epsilon from A and B for each vdw type's interaction with itself
      Real A; Real B; Real A14; Real B14;
      if (get_vdw_pair_params(index, index, &A, &B, &A14, &B14) ) {
        if (A && B) {
          *sigma = sqrt(cbrt(A)) / sqrt(cbrt(B));
          *epsilon = B*B / (4*A);
        }
        else {
          *sigma = 0; *epsilon = 0;
        }
        if (A14 && B14) {
          *sigma14 = sqrt(cbrt(A14)) / sqrt(cbrt(B14));
          *epsilon14 = B14*B14 / (4*A14);
        }
        else {
          *sigma14 = 0; *epsilon14 = 0;
        }
      }
      else {NAMD_die ("Function get_vdw_params failed to derive Lennard-Jones sigma and epsilon from A and B values\n");}
    }
  }

        int get_vdw_pair_params(Index ind1, Index ind2, Real *, Real *, Real *, Real *);
                                                //  Find a vwd_pair parameter

        int get_num_vdw_params(void) { return NumVdwParamsAssigned; }

  int get_table_pair_params(Index, Index, int*);

        //  The print_*_params are provided for debugging purposes
        void print_bond_params();               //  Print bonds params
        void print_angle_params();              //  Print angle params
        void print_dihedral_params();           //  Print dihedral params
        void print_dihedral_array();            //  Print dihedral params post pocessed
        void print_improper_params();           //  Print improper params
        void print_crossterm_params();          //  Print cross-term params
        void print_vdw_params();                //  Print vdw params
        void print_vdw_pair_params();           //  Print vdw_pair params
        void print_nbthole_pair_params();           //  Print nbthole_pair params
        void print_param_summary();             //  Print a summary of params
        void read_ener_table(SimParameters*); // Read an energy table file
  int get_int_table_type(char*); // Return the integer type for a named table interaction

  int read_energy_type(FILE*, const int, BigReal*, const float, const float);
  int read_energy_type_cubspline(FILE*, const int, BigReal*, const float, const float);
  int read_energy_type_bothcubspline(FILE*, const int, BigReal*, const float, const float);
};

#endif