CompressPsf.h File Reference

#include "structures.h"
#include <string>
#include <deque>
#include <ckhashtable.h>

Go to the source code of this file.

Classes
struct	OutputAtomRecord
struct	OutputAtomRecord::shortVals
struct	OutputAtomRecord::integerVals
struct	OutputAtomRecord::floatVals
class	HashPoolAdaptorT< T >
class	HashPool< T >

Macros
#define	COMPRESSED_PSF_VER   1.72
#define	COMPRESSED_PSF_MAGICNUM   1234

Functions
void	compress_molecule_info (Molecule *mol, char *psfFileName, Parameters *param, SimParameters *simParam, ConfigList *cfgList)
void	flipNum (char *elem, int elemSize, int numElems)
template<typename T >
int	lookupCstPool (const std::vector< T > &pool, const T &val)

Macro Definition Documentation

COMPRESSED_PSF_MAGICNUM

#define COMPRESSED_PSF_MAGICNUM   1234

Definition at line 13 of file CompressPsf.h.

Referenced by outputCompressedFile().

COMPRESSED_PSF_VER

#define COMPRESSED_PSF_VER   1.72

Definition at line 9 of file CompressPsf.h.

Referenced by outputCompressedFile().

Function Documentation

compress_molecule_info()

void compress_molecule_info	(	Molecule *	mol,
		char *	psfFileName,
		Parameters *	param,
		SimParameters *	simParam,
		ConfigList *	cfgList
	)

Definition at line 436 of file CompressPsf.C.

References buildExclusions(), g_cfgList, g_mol, g_param, g_simParam, integrateAllAtomSigs(), loadMolInfo(), and outputCompressedFile().

Referenced by NamdState::loadStructure().

{
    g_mol = mol;
    g_param = param;
    g_simParam = simParam; //used for building exclusions
    g_cfgList = cfgList; //used for integrating extra bonds

    //read psf files
    //readPsfFile(psfFileName);
    loadMolInfo();

    integrateAllAtomSigs();

    buildExclusions();

    //buildParamData();

    char *outFileName = new char[strlen(psfFileName)+20];
    sprintf(outFileName, "%s.inter", psfFileName);
    //the text file for signatures and other non-per-atom info
    FILE *txtOfp = fopen(outFileName, "w");
    sprintf(outFileName, "%s.inter.bin", psfFileName);
    //the binary file for per-atom info
    FILE *binOfp = fopen(outFileName, "wb");
    delete [] outFileName;

    //output compressed psf file
    outputCompressedFile(txtOfp, binOfp);

    fclose(txtOfp);
    fclose(binOfp);
}

flipNum()

void flipNum	(	char *	elem,
		int	elemSize,
		int	numElems
	)

Definition at line 406 of file CompressPsf.C.

Referenced by OutputAtomRecord::flip().

                                                    {
    int mid = elemSize/2;
    char *ptr = elem;
    for(int i=0; i<numElems; i++) {
        for(int j=0; j<mid; j++) {
            char tmp = ptr[j];
            ptr[j] = ptr[elemSize-1-j];
            ptr[elemSize-1-j] = tmp;
        }
        ptr += elemSize;
    }
}

lookupCstPool()

template<typename T >

int lookupCstPool	(	const std::vector< T > &	pool,
		const T &	val
	)

Definition at line 56 of file CompressPsf.h.

Referenced by buildBondData().

{
    for(int i=0; i<pool.size(); i++)
    {
        if(pool[i]==val)
            return i;
    }
    return -1;
}