structures.h

Go to the documentation of this file.

#ifndef STRUCTURES_H
#define STRUCTURES_H

#include "common.h"
#include <vector>


// status elements, used for Atom status 
#define UnknownAtom      0x00
#define HydrogenAtom     0x01
#define OxygenAtom       0x02
#define HBDonorAtom      0x04
#define HBAcceptorAtom   0x08
#define HBAntecedentAtom 0x10
#define HBHydrogenAtom   0x20
#define LonepairAtom     0x40
#define DrudeAtom        0x80


typedef int Index;              //  Used for index into arrays
                                        //  or parameters

typedef struct atom_name_info
{
        char *resname;
        char *atomname;
        char *atomtype;
} AtomNameInfo;

typedef struct atom_constants
{
        Real mass;
        Real charge;
        Index vdw_type;
        int32 status;            // flags telling about this atom
        int32 partner;             // connecting atom, for hydrogens
        int32 hydrogenList;     // index of atom in hydrogenGroup list
} Atom;

typedef struct bond
{
        int32 atom1;
        int32 atom2;
        Index bond_type;
} Bond;

typedef struct angle
{
        int32 atom1;
        int32 atom2;
        int32 atom3;
        Index angle_type;
} Angle;

typedef struct dihedral
{
        int32 atom1;
        int32 atom2;
        int32 atom3;
        int32 atom4;
        Index dihedral_type;
} Dihedral;

typedef struct improper
{
        int32 atom1;
        int32 atom2;
        int32 atom3;
        int32 atom4;
        Index improper_type;
} Improper;

typedef struct crossterm
{
        int32 atom1;
        int32 atom2;
        int32 atom3;
        int32 atom4;
        int32 atom5;
        int32 atom6;
        int32 atom7;
        int32 atom8;
        Index crossterm_type;
} Crossterm;

typedef struct gromacsPair
{
    int32 atom1;
    int32 atom2;
    Real pairC12;
    Real pairC6;
    Index gromacsPair_type;
} GromacsPair;


// DRUDE: data read from PSF
typedef struct drude_constants  // supplement Atom data
{                        // create array length N of these
  Real alpha;
  Real thole;
} DrudeConst;

typedef struct lphost    // lone pair host
{
  int32 atom1;
  int32 atom2;
  int32 atom3;
  int32 atom4;
  Real distance;
  Real angle;
  Real dihedral;
} Lphost;

typedef struct aniso     // anisotropic term
{
  int32 atom1;
  int32 atom2;
  int32 atom3;
  int32 atom4;
  Real k11;
  Real k22;
  Real k33;
} Aniso;

typedef struct thole    // Thole terms - constructed implicitly from exclusions
{
  int32 atom1;  // first heavy atom
  int32 atom2;  // Drude particle of first heavy atom
  int32 atom3;  // second heavy atom
  int32 atom4;  // Drude particle of second heavy atom
  Real aa;      // constant (alpha_i * alpha_j)^(-6) / (thole_i + thole_j)
  Real qq;      // combined charge of Drudes (C * q_{i+1} * q_{j+1})
} Thole;
// DRUDE


class Exclusion
{
public:
        Exclusion(void) : modified(0) {;}
        Exclusion(int a1, int a2, int mod = 0) :
                atom1(a1), atom2(a2), modified(mod) {;}
        int32 atom1;
        int32 atom2;
        Index modified;
        int hash(void) const
        {
                return atom1 + atom2;
        }
        int operator==(const Exclusion &o) const
        {
                return atom1 == o.atom1 && atom2 == o.atom2;
        }
        int operator<(const Exclusion &o) const
        {
                return
                (
                  ( atom1 < o.atom1 ) ||
                  ( atom1 == o.atom1 && atom2 < o.atom2 )
                );
        }
};


class MOStream;
class MIStream;

enum TupleSigType {BOND=0, ANGLE, DIHEDRAL, IMPROPER, DONOR, ACCEPTOR, CROSSTERM, EXCLUSION};

inline unsigned int circShift(unsigned int h, unsigned int by) {
  const unsigned int intBits=8*sizeof(unsigned int);
  by%=intBits;
  return (h<<by)|(h>>(intBits-by));
}

class TupleSignature{
public:
    //This field indicates which class this tuple belongs to (bond or angle or ...)
    TupleSigType tupleType;
    int numOffset;
    //the relative offset from the atom index
    int *offset;   

    //This type is determined by the Parameter object
    //for Exclusion, this indicates the modified field
    Index tupleParamType;

    //indicate this tuple is specified in the psf file, not from other files.
    //this is added due to the extraBonds feature. All tuples from extraBonds
    //are not real!
    char isReal;

public:
    TupleSignature(){        
        offset = NULL;
        isReal = 1;
    }

    TupleSignature(int n, TupleSigType t, Index paramType, char ir=1){
        tupleType = t;
        numOffset = n;
        offset = new int[n];        
        tupleParamType = paramType;
        isReal = ir;
    }
    TupleSignature(const TupleSignature& oneSig){
        tupleType = oneSig.tupleType;
        numOffset = oneSig.numOffset;
        offset = new int[numOffset];
        setOffsets(oneSig.offset);        
        tupleParamType = oneSig.tupleParamType;
        isReal = oneSig.isReal;
    }
    TupleSignature &operator=(const TupleSignature& oneSig){
        tupleType = oneSig.tupleType;
        numOffset = oneSig.numOffset;
        if(offset) delete [] offset;
        offset = new int[numOffset];
        setOffsets(oneSig.offset);        
        tupleParamType = oneSig.tupleParamType;
        isReal = oneSig.isReal;
        return *this;
    }
    int operator==(const TupleSignature& sig) const{
            if(tupleType!=sig.tupleType)
                return 0;

            if(tupleParamType != sig.tupleParamType)
                return 0;

        if(isReal != sig.isReal)
            return 0;

                if(numOffset != sig.numOffset) return 0;
                
            int equalCnt=0;
                    
            for(int i=0; i<numOffset; i++){
                equalCnt += (offset[i]==sig.offset[i]);      
            }
            return equalCnt==numOffset;
        }
    ~TupleSignature(){
        if(offset) delete[] offset;
    }
    void setOffsets(int *offs){
        for(int i=0; i<numOffset; i++)
            offset[i] = offs[i];
        //sort the offset in increasing order
        //based on the input files, this offset is almost sorted increasingly
        //Therefore using insertion sort
        /*switch(numOffset){
            case 1:
                break;
            case 2:
                if(offset[0]>offset[1]){
                    int tmp = offset[0];
                    offset[0] = offset[1];
                    offset[1] = tmp;
                }
                break;
            default: //insertion sort
                for(int ii=1; ii<numOffset; ii++){
                    int val = offset[ii];
                    for(int jj=ii-1; jj>=0; jj--){
                        if(offset[jj]<val){
                            offset[jj+1] = offset[jj];
                            offset[jj] = val;
                        }else
                            break;
                    }
                }
        }*/
    }
    void setEmpty(){
        delete [] offset;
        offset = NULL;
    }
    int isEmpty(){
        return offset==NULL;
    }
    void output(FILE *ofp){
        for(int i=0; i<numOffset; i++)
            fprintf(ofp, "%d ", offset[i]);
        fprintf(ofp, "| %d | %d\n", tupleParamType, isReal);         
    }
  
    int hash() const {
      unsigned int code = tupleType;
      unsigned int codesz = 8 * sizeof(int);
      unsigned int shift = codesz / numOffset;
      
      if (shift == 0) shift=1;
      unsigned int i;
      for(i=0; i < numOffset; i++) {
        code = circShift(code,shift);
        code ^= offset[i];
      }
      return code;
    }
  
    void pack(MOStream *msg);
    void unpack(MIStream *msg);
};

//represents the signatures for atoms
class AtomSignature{
public:
    int bondCnt;
    int angleCnt;
    int dihedralCnt;
    int improperCnt;
    int crosstermCnt;
    // JLai
    int gromacsPairCnt;

    TupleSignature *bondSigs;
    TupleSignature *angleSigs;
    TupleSignature *dihedralSigs;
    TupleSignature *improperSigs;
    TupleSignature *crosstermSigs;
    // JLai
    TupleSignature *gromacsPairSigs;

    AtomSignature(){
        bondCnt=angleCnt=dihedralCnt=improperCnt=crosstermCnt=0;
        // JLai
        gromacsPairCnt=0;
        bondSigs = NULL;
        angleSigs = NULL;
        dihedralSigs = NULL;
        improperSigs = NULL;
        crosstermSigs = NULL;
        // JLai
        gromacsPairSigs = NULL;
    }
    AtomSignature(const AtomSignature &sig){
        bondSigs = NULL;
        angleSigs = NULL;
        dihedralSigs = NULL;
        improperSigs = NULL;
        crosstermSigs = NULL;
        // JLai
        gromacsPairSigs = NULL;

        bondCnt = sig.bondCnt;
        if(bondCnt>0){            
            bondSigs = new TupleSignature[bondCnt];
            for(int i=0; i<bondCnt; i++)
                bondSigs[i] = sig.bondSigs[i];
        }

        angleCnt = sig.angleCnt;
        if(angleCnt>0){            
            angleSigs = new TupleSignature[angleCnt];
            for(int i=0; i<angleCnt; i++)
                angleSigs[i] = sig.angleSigs[i];
        }
        
        dihedralCnt = sig.dihedralCnt;
        if(dihedralCnt>0){            
            dihedralSigs = new TupleSignature[dihedralCnt];
            for(int i=0; i<dihedralCnt; i++)
                dihedralSigs[i] = sig.dihedralSigs[i];
        }
        
        improperCnt = sig.improperCnt;
        if(improperCnt>0){
            improperSigs = new TupleSignature[improperCnt];
            for(int i=0; i<improperCnt; i++)
                improperSigs[i] = sig.improperSigs[i];
        }      

        crosstermCnt = sig.crosstermCnt;
        if(crosstermCnt>0){
            crosstermSigs = new TupleSignature[crosstermCnt];
            for(int i=0; i<crosstermCnt; i++)
                crosstermSigs[i] = sig.crosstermSigs[i];
        }        

        // JLai
        gromacsPairCnt = sig.gromacsPairCnt;
        if(gromacsPairCnt>0){
            gromacsPairSigs = new TupleSignature[gromacsPairCnt];
            for(int i=0; i<gromacsPairCnt; i++) {
                gromacsPairSigs[i] = sig.gromacsPairSigs[i];
            }
        }
    }
    AtomSignature& operator=(const AtomSignature& sig){        
        bondCnt = sig.bondCnt;
        if(bondSigs) delete [] bondSigs;
        if(bondCnt>0){
            bondSigs = new TupleSignature[bondCnt];
            for(int i=0; i<bondCnt; i++)
                bondSigs[i] = sig.bondSigs[i];
        }else
            bondSigs = NULL;

        angleCnt = sig.angleCnt;
        if(angleSigs) delete [] angleSigs;
        if(angleCnt>0){
            angleSigs = new TupleSignature[angleCnt];
            for(int i=0; i<angleCnt; i++)
                angleSigs[i] = sig.angleSigs[i];
        }else
            angleSigs = NULL;
        
        dihedralCnt = sig.dihedralCnt;
        if(dihedralSigs) delete [] dihedralSigs;
        if(dihedralCnt>0){
            dihedralSigs = new TupleSignature[dihedralCnt];
            for(int i=0; i<dihedralCnt; i++)
                dihedralSigs[i] = sig.dihedralSigs[i];
        }else
            dihedralSigs = NULL;
        
        improperCnt = sig.improperCnt;
        if(improperSigs) delete [] improperSigs;
        if(improperCnt>0){
            improperSigs = new TupleSignature[improperCnt];
            for(int i=0; i<improperCnt; i++)
                improperSigs[i] = sig.improperSigs[i];
        }else
            improperSigs = NULL;      

        crosstermCnt = sig.crosstermCnt;
        if(crosstermSigs) delete [] crosstermSigs;
        if(crosstermCnt>0){
            crosstermSigs = new TupleSignature[crosstermCnt];
            for(int i=0; i<crosstermCnt; i++)
                crosstermSigs[i] = sig.crosstermSigs[i];
        }else
            crosstermSigs = NULL;

        // JLai
        gromacsPairCnt = sig.gromacsPairCnt;
        if(gromacsPairSigs) delete [] gromacsPairSigs;
        if(gromacsPairCnt>0){
            gromacsPairSigs = new TupleSignature[gromacsPairCnt];
            for(int i=0; i<gromacsPairCnt; i++)
                gromacsPairSigs[i] = sig.gromacsPairSigs[i];
        }else
            gromacsPairSigs = NULL;

        return *this;
    }
    int operator==(const AtomSignature& sig) const{
            if(bondCnt!=sig.bondCnt) return 0;
            if(angleCnt!=sig.angleCnt) return 0;
            if(dihedralCnt!=sig.dihedralCnt) return 0;
            if(improperCnt!=sig.improperCnt) return 0;
            if(crosstermCnt!=sig.crosstermCnt) return 0;
            //JLai
            if(gromacsPairCnt!=sig.gromacsPairCnt) return 0;
        
        #define CMPSIGS(TUPLE) \
        for(int i=0; i<sig.TUPLE##Cnt; i++){ \
            if(!(TUPLE##Sigs[i]==sig.TUPLE##Sigs[i])) return 0; \
        } \
        
            CMPSIGS(bond)
            CMPSIGS(angle)
            CMPSIGS(dihedral)
            CMPSIGS(improper)
            CMPSIGS(crossterm)
            // JLai
            CMPSIGS(gromacsPair)
        
            return 1;
        }
    ~AtomSignature(){
        if(bondSigs) delete[] bondSigs;
        if(angleSigs) delete[] angleSigs;
        if(dihedralSigs) delete[] dihedralSigs;
        if(improperSigs) delete[] improperSigs;
        if(crosstermSigs) delete[] crosstermSigs;
        // JLai
        if(gromacsPairSigs) delete[] gromacsPairSigs;
    }    

    void removeEmptyTupleSigs();
    void pack(MOStream *msg);
    void unpack(MIStream *msg);
};

struct AtomNameIdx{
    Index resnameIdx;
    Index atomnameIdx;
    Index atomtypeIdx;
};
struct AtomCstInfo{
    Index vdw_type;
    int32 status;
    int32 partner;
    int32 hydrogenList;
};

struct ExclusionSignature{
    int fullExclCnt; //1-2, 1-3 exclusion
    int *fullOffset; //should be in increasing order
    int modExclCnt; //1-4 exclusion
    int *modOffset; //should be in increasing order
#ifdef NAMD_CUDA
    int allExclCnt;
    TupleSignature *allTuples;
#endif

    ExclusionSignature(){
        fullExclCnt = modExclCnt = 0;
        fullOffset = modOffset = NULL;
#ifdef NAMD_CUDA
        allExclCnt = 0;
        allTuples = NULL;
#endif
    }    
    ExclusionSignature(const ExclusionSignature& sig){
        fullOffset = modOffset = NULL;
        fullExclCnt = sig.fullExclCnt;
        if(fullExclCnt>0){
            fullOffset = new int[fullExclCnt];
            for(int i=0; i<fullExclCnt; i++)
                fullOffset[i] = sig.fullOffset[i];
        }
        
        modExclCnt = sig.modExclCnt;
        if(modExclCnt>0){
            modOffset = new int[modExclCnt];
            for(int i=0; i<modExclCnt; i++)
                modOffset[i] = sig.modOffset[i];
        }
#ifdef NAMD_CUDA
        allTuples = NULL;
        allExclCnt = sig.allExclCnt;
        if(allExclCnt>0){
            allTuples = new TupleSignature[allExclCnt];
            for(int i=0; i<allExclCnt; i++)
                allTuples[i] = sig.allTuples[i];
        }
#endif
    }
    ~ExclusionSignature(){
        if(fullOffset) delete [] fullOffset;
        if(modOffset) delete [] modOffset;
#ifdef NAMD_CUDA
        if(allTuples) delete [] allTuples;
#endif
    }
    
    ExclusionSignature& operator=(const ExclusionSignature& sig){
        fullExclCnt = sig.fullExclCnt;
        if(fullOffset) delete [] fullOffset;
        if(fullExclCnt>0){
            fullOffset = new int[fullExclCnt];
            for(int i=0; i<fullExclCnt; i++)
                fullOffset[i] = sig.fullOffset[i];
        }else
            fullOffset = NULL;
    
        modExclCnt = sig.modExclCnt;
        if(modOffset) delete [] modOffset;
        if(modExclCnt>0){
            modOffset = new int[modExclCnt];
            for(int i=0; i<modExclCnt; i++)
                modOffset[i] = sig.modOffset[i];
        }else
            modOffset = NULL;
#ifdef NAMD_CUDA
        allExclCnt = sig.allExclCnt;
        if(allTuples) delete [] allTuples;
        if(allExclCnt>0){
            allTuples = new TupleSignature[allExclCnt];
            for(int i=0; i<allExclCnt; i++)
                allTuples[i] = sig.allTuples[i];
        }else
            allTuples = NULL;
#endif

        return *this;
    }
        int operator==(const ExclusionSignature& sig) const{
            if(fullExclCnt!=sig.fullExclCnt) return 0;
            if(modExclCnt!=sig.modExclCnt) return 0;
            
            for(int i=0; i<fullExclCnt; i++){
                        if(fullOffset[i]!=sig.fullOffset[i]) return 0;
            }
            for(int i=0; i<modExclCnt; i++){
                        if(modOffset[i]!=sig.modOffset[i]) return 0;
            }
            return 1;
        }
    //both input should be sorted in increasing order
    void setOffsets(std::vector<int>& fullVec, std::vector<int>& modVec){
        fullExclCnt = fullVec.size();
        modExclCnt = modVec.size();
        if(fullExclCnt>0) {        
            fullOffset = new int[fullExclCnt];
            for(int i=0; i<fullExclCnt; i++)
                fullOffset[i] = fullVec[i];
        }

        if(modExclCnt>0) {        
            modOffset = new int[modExclCnt];
            for(int i=0; i<modExclCnt; i++)
                modOffset[i] = modVec[i];       
        }
#ifdef NAMD_CUDA
        buildTuples();
    }
    void buildTuples() {
        delete [] allTuples;
        allTuples = NULL;
        allExclCnt = 0;
        for(int i=0; i<fullExclCnt; i++)
            if ( fullOffset[i] > 0 ) ++allExclCnt;
        for(int i=0; i<modExclCnt; i++)
            if ( modOffset[i] > 0 ) ++allExclCnt;
        if(allExclCnt>0){
            allTuples = new TupleSignature[allExclCnt];
            int j = 0;
            for(int i=0; i<fullExclCnt; i++){
                if ( fullOffset[i] <= 0 ) continue;
                TupleSignature oneSig(1,EXCLUSION,0);
                oneSig.offset[0] = fullOffset[i];
                allTuples[j++] = oneSig;
            }
            for(int i=0; i<modExclCnt; i++){
                if ( modOffset[i] <= 0 ) continue;
                TupleSignature oneSig(1,EXCLUSION,1);
                oneSig.offset[0] = modOffset[i];
                allTuples[j++] = oneSig;
            }
        }
#endif
    }

    int hash() const {
      unsigned int numOffset = fullExclCnt + modExclCnt;
      unsigned int code = 0x12345678;
      unsigned int codesz = 8 * sizeof(int);
      unsigned int shift = codesz / numOffset;
    
      if (shift == 0) shift=1;
      unsigned int i;
      for(i=0; i < fullExclCnt; i++) {
        code = circShift(code,shift);
        code ^= fullOffset[i];
      }
      for(i=0; i < modExclCnt; i++) {
        code = circShift(code,shift);
        code ^= modOffset[i];
      }
      return code;
    }
  
  void removeEmptyOffset();
    //assuming offsets in the signature have been sorted increasingly
    int findOffset(int offset, int  *fullOrMod);
    void pack(MOStream *msg);
    void unpack(MIStream *msg);
};

#endif

---