Output.h

Go to the documentation of this file.

/*
   This object outputs the data collected on the master  node
*/

#ifndef OUTPUT_H
#define OUTPUT_H

#include "common.h"
#include <string>
#include <map>

class Vector;
class FloatVector;
class Lattice;
class ReplicaDcdInitMsg;
class ReplicaDcdDataMsg;

// semaphore "steps", must be negative
#define FILE_OUTPUT -1
#define END_OF_RUN -2
#define EVAL_MEASURE -3
#define FORCE_OUTPUT -4

#define OUTPUT_SINGLE_FILE 1
#define OUTPUT_MAGIC_NUMBER 123456
#define OUTPUT_FILE_VERSION 1.00


class Output 
{

private:

friend class SimParameters;

   //  output coords to dcd file
   //  Pass non-NULL Lattice to include unit cell in the timesteps.
   int output_dcdfile(int, int, FloatVector *, const Lattice *, int dcdIndex);
   void output_veldcdfile(int, int, FloatVector *);     //  output velocities to
                                                //  dcd file
   void output_forcedcdfile(int, int, FloatVector *); //  output forces to
                                                //  dcd file

   void output_restart_coordinates(Vector *, int, int);
                                                //  output coords to 
                                                //  restart file
   void output_restart_velocities(int, int, Vector *);
                                                //  output velocities to 
                                                //  restart file
   void output_final_coordinates(Vector *, int, int);//  output final coordinates
   void output_final_velocities(int, int, Vector *);    //  output final coordinates
   void output_forces(int, int, Vector *);      //  output forces

   void scale_vels(Vector *, int, Real);        //  scale velocity vectors before output
   void scale_fvels(FloatVector *, int, Real);  //  scale velocity vectors before output / IMD send
   void write_binary_file(char *, int, Vector *); // Write a binary restart file with
                                                //  coordinates or velocities

   struct replicaDcdFile {
     std::string filename;
     int fileid;
     replicaDcdFile() : fileid(0) { ; }
   };
   std::map<int,replicaDcdFile> replicaDcdFiles;
   std::map<std::pair<int,uint16_t>,replicaDcdFile> replicaDcdSelectFiles;
   int replicaDcdActive;
   int replicaDcdIndex;

public :
   Output();                                    //  Constructor
   ~Output();                                   //  Destructor
   void energy(int, BigReal *);                 //  Output energies

  static std::pair<int,int> coordinateNeeded(int timestep);
  void coordinate(int timestep, int n, Vector *coor,
                  FloatVector *fcoor, Lattice &lattice);
  static int velocityNeeded(int timestep);
  void velocity(int timestep, int n, Vector *vel, FloatVector *fvel);
  static int forceNeeded(int timestep);
  void force(int timestep, int n, Vector *frc, FloatVector *ffrc);

  void replicaDcdOff() { replicaDcdActive = 0; }
  void setReplicaDcdIndex(int index);
  void replicaDcdInit(int index, const char *filename);
  void replicaDcdSelectInit(int index, const char *tag, const char *filename);
  void recvReplicaDcdInit(ReplicaDcdInitMsg *msg);
  void recvReplicaDcdData(ReplicaDcdDataMsg *msg);
};

#ifdef MEM_OPT_VERSION
class ParOutput{
private:
    void output_veldcdfile_master(int timestep, int n);
    void output_veldcdfile_slave(int timestep, int fID, int tID, Vector *vecs);
    void output_restart_velocities_master(int timestep, int n);
    void output_restart_velocities_slave(int timestep, int fID, int tID, Vector *vecs, int64 offset);
    void output_final_velocities_master(int n);
    void output_final_velocities_slave(int fID, int tID, Vector *vecs, int64 offset);

    void output_forcedcdfile_master(int timestep, int n);
    void output_forcedcdfile_slave(int timestep, int fID, int tID, Vector *vecs);
    void output_forces_master(int n);
    void output_forces_slave(int fID, int tID, Vector *vecs, int64 offset);
    void output_dcdfile_master(int timestep, int n, const Lattice *lat, int tag);
    void output_dcdfile_slave(int timestep, int fID, int tID, FloatVector *fvecs, int tag);
    void output_restart_coordinates_master(int timestep, int n);
    void output_restart_coordinates_slave(int timestep, int fID, int tID, Vector *vecs, int64 offset);
    void output_final_coordinates_master(int n);
    void output_final_coordinates_slave(int fID, int tID, Vector *vecs, int64 offset);

    void write_binary_file_master(char *fname, int n);
    void write_binary_file_slave(char *fname, int fID, int tID, Vector *vecs, int64 offset);

        #if !OUTPUT_SINGLE_FILE
        char *buildFileName(OUTPUTFILETYPE type, int timestep=-9999);
        #endif

    int dcdFileID;
    Bool dcdFirst;
    float *dcdX, *dcdY, *dcdZ;
    size_t dcdAllocSize;
    int veldcdFileID;
    Bool veldcdFirst;    
    float *veldcdX, *veldcdY, *veldcdZ;
    int forcedcdFileID;
    Bool forcedcdFirst;    
    float *forcedcdX, *forcedcdY, *forcedcdZ;
    Bool cleanUpXYZ;
    int outputID; //the sequence of this output
    Bool parFirst[16];
    int parFileid[16];  //  File id for the dcd file
    off_t dcdSelectionOffsets[16];  // each dcdselection file offset
    size_t dcdSelectionLocalSize[16];  // number of points per dcdselection
    std::vector<uint32> dcdSelectionMap[16]; //local offset -> global idx map
public:
    ParOutput(int oid=-1){
        dcdFileID=veldcdFileID=-99999;
        forcedcdFileID=-99999;
        dcdFirst=veldcdFirst=TRUE;
        forcedcdFirst=TRUE;
        dcdX=dcdY=dcdZ=veldcdX=veldcdY=veldcdZ=NULL;
        forcedcdX=forcedcdY=forcedcdZ=NULL;
                outputID=oid;
                cleanUpXYZ=true;
        for(int i=0;i<16;i++)
          parFirst[i]=true;
        dcdAllocSize=0;
    }
    ~ParOutput() {}

    void velocityMaster(int timestep, int n);
    void velocitySlave(int timestep, int fID, int tID, Vector *vecs);

    void forceMaster(int timestep, int n);
    void forceSlave(int timestep, int fID, int tID, Vector *vecs);

    void coordinateMaster(int timestep, int n, Lattice &lat);
    void coordinateSlave(int timestep, int fID, int tID, Vector *vecs, FloatVector *fvecs);
    void setDcdSelectionParams(int index, off_t offset, size_t size, std::vector<uint32> map );
};
#endif

#endif