dcdlib.C File Reference

#include "dcdlib.h"

Go to the source code of this file.

Macros
#define	OUTPUT_SINGLE_FILE   1
#define	NAMD_write   NAMD_write64
#define	LSEEK   lseek
#define	READ   read
#define	LSEEK   NAMD_seek
#define	O_LARGEFILE   0x0
#define	CHECK_FREAD(X, msg)
#define	CHECK_FEOF(X, msg)
#define	NFILE_POS   ((OFF_T) 8)
#define	NPRIV_POS   ((OFF_T) 12)
#define	NSAVC_POS   ((OFF_T) 16)
#define	NSTEP_POS   ((OFF_T) 20)

Functions
void	NAMD_write (int fd, const char *buf, size_t count)
OFF_T	NAMD_seek (int file, OFF_T offset, int whence)
void	pad (char *s, int len)
int	open_dcd_read (char *filename)
int	open_dcd_write (const char *dcdname)
int	open_dcd_write_par_slave (char *dcdname)
int	write_dcdstep (int fd, int N, float *X, float *Y, float *Z, double *cell)
int	write_dcdstep_par_cell (int fd, double *cell)
int	write_dcdstep_par_XYZUnits (int fd, int N)
int	update_dcdstep_par_header (int fd)
int	write_dcdstep_par_slave (int fd, int parL, int parU, int N, float *X, float *Y, float *Z)
int	write_dcdheader (int fd, const char *filename, int N, int NFILE, int NPRIV, int NSAVC, int NSTEP, double DELTA, int with_unitcell)
int	get_dcdheader_size ()
void	close_dcd_read (int fd, int num_fixed, int *indexes)
void	close_dcd_write (int fd)

Macro Definition Documentation

CHECK_FEOF

#define CHECK_FEOF	(		X,
			msg
	)

Value:

if (X==0) \
                             { \
                                return(DCD_BADEOF); \
                             }

Definition at line 97 of file dcdlib.C.

CHECK_FREAD

#define CHECK_FREAD	(		X,
			msg
	)

Value:

if (X==-1) \
                             { \
                                return(DCD_BADREAD); \
                             }

Definition at line 80 of file dcdlib.C.

LSEEK [1/2]

#define LSEEK   lseek

Definition at line 61 of file dcdlib.C.

Referenced by NAMD_seek(), update_dcdstep_par_header(), write_dcdstep(), write_dcdstep_par_slave(), and write_dcdstep_par_XYZUnits().

LSEEK [2/2]

#define LSEEK   NAMD_seek

Definition at line 61 of file dcdlib.C.

NAMD_write

#define NAMD_write   NAMD_write64

Definition at line 24 of file dcdlib.C.

Referenced by ofstream_namd::flush(), update_dcdstep_par_header(), write_dcdheader(), write_dcdstep(), write_dcdstep_par_cell(), write_dcdstep_par_slave(), and write_dcdstep_par_XYZUnits().

NFILE_POS

#define NFILE_POS   ((OFF_T) 8)

Definition at line 628 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

NPRIV_POS

#define NPRIV_POS   ((OFF_T) 12)

Definition at line 629 of file dcdlib.C.

NSAVC_POS

#define NSAVC_POS   ((OFF_T) 16)

Definition at line 630 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

NSTEP_POS

#define NSTEP_POS   ((OFF_T) 20)

Definition at line 631 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

O_LARGEFILE

#define O_LARGEFILE   0x0

Definition at line 64 of file dcdlib.C.

Referenced by open_dcd_read(), open_dcd_write(), and open_dcd_write_par_slave().

OUTPUT_SINGLE_FILE

#define OUTPUT_SINGLE_FILE   1

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 16 of file dcdlib.C.

READ

#define READ   read

Definition at line 46 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

Function Documentation

close_dcd_read()

void close_dcd_read	(	int	fd,
		int	num_fixed,
		int *	indexes
	)

Definition at line 1033 of file dcdlib.C.

{
#ifdef WIN32
        _close(fd);
#else
        close(fd);
#endif

        if (num_fixed)
        {
                delete [] indexes;
        }
}

close_dcd_write()

void close_dcd_write

(

int

fd

)

Definition at line 1063 of file dcdlib.C.

References NAMD_err().

Referenced by Output::recvReplicaDcdInit(), and ComputeQMMgr::~ComputeQMMgr().

{
#ifdef WIN32
  if ( _close(fd) )
#else
  if ( fsync(fd) || close(fd) )
#endif
  {
    NAMD_err("Error closing DCD file");
  }
}

get_dcdheader_size()

int get_dcdheader_size

(

)

Definition at line 1005 of file dcdlib.C.

                        {
        int headersize = 0;
        int totalInt32s = 27; /* 27 writes from out_integer */
        int totalChars = 164; /* 3 writes from title_string */
        int totalFloats = 1; /* 1 write from out_float */
        headersize = sizeof(int32)*totalInt32s+totalChars+sizeof(float)*totalFloats;
        return headersize;
}

NAMD_seek()

OFF_T NAMD_seek	(	int	file,
		OFF_T	offset,
		int	whence
	)

Definition at line 49 of file dcdlib.C.

References LSEEK, NAMD_die(), NAMD_err(), and OFF_T.

                                                    {
  OFF_T retval = LSEEK(file, offset, whence);
  if ( retval < 0 ) NAMD_err("seek failed while writing DCD file");
  if ( whence == SEEK_SET && retval != offset ) {
    char buf[256];
    sprintf(buf, "seek failed while writing DCD file: SEEK_SET %lld returned %lld\n", offset, retval);
    NAMD_die(buf);
  }
  return retval;
}

NAMD_write()

void NAMD_write	(	int	fd,
		const char *	buf,
		size_t	count
	)

Definition at line 26 of file dcdlib.C.

References NAMD_bug(), and NAMD_die().

                                                       {
  while ( count ) {
#if defined(WIN32) && !defined(__CYGWIN__)
    long retval = _write(fd,buf,count);
#else
    ssize_t retval = write(fd,buf,count);
#endif
    if ( retval < 0 && errno == EINTR ) retval = 0;
    if ( retval < 0 ) NAMD_die(strerror(errno));
    if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write64()");
    buf += retval;
    count -= retval;
  }
}

open_dcd_read()

int open_dcd_read

(

char *

filename

)

Definition at line 145 of file dcdlib.C.

References DCD_DNE, DCD_OPENFAILED, and O_LARGEFILE.

{
        int dcdfd;              /*  file descriptor for dcd file        */

        /*  Do a stat just to see if the file really exists     */
        if (access(filename, F_OK) != 0)
        {
                if (errno == ENOENT)
                {
                        return(DCD_DNE);
                }
        }

        /*  Try and open the file                               */
#ifdef WIN32
        dcdfd=_open(filename, O_RDONLY|O_BINARY|O_LARGEFILE);
#else
        dcdfd=open(filename, O_RDONLY|O_LARGEFILE);
#endif

        if (dcdfd == -1)
        {
                return(DCD_OPENFAILED);
        }

        return(dcdfd);
}

open_dcd_write()

int open_dcd_write

(

const char *

dcdname

)

Definition at line 662 of file dcdlib.C.

References DCD_OPENFAILED, NAMD_backup_file(), and O_LARGEFILE.

Referenced by open_dcd_write_par_slave(), ComputeQMMgr::recvPartQM(), and Output::recvReplicaDcdData().

{
        int dcdfd;
        NAMD_backup_file(dcdname,".BAK");

#ifdef WIN32
        while ( (dcdfd = _open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_LARGEFILE,
                                _S_IREAD|_S_IWRITE)) < 0)
#else
#ifdef NAMD_NO_O_EXCL
        while ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE,
#else
        while ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_LARGEFILE,
#endif
                                S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
#endif
        {
                if ( errno != EINTR ) return(DCD_OPENFAILED);
        }

        return(dcdfd);
}

open_dcd_write_par_slave()

int open_dcd_write_par_slave

(

char *

dcdname

)

Definition at line 689 of file dcdlib.C.

References DCD_OPENFAILED, O_LARGEFILE, and open_dcd_write().

{
#if OUTPUT_SINGLE_FILE
        //In the case of single file, the dcd output by slaves has been created
        //by the master, so the dcd file doesn't need to be created again and
        //backed up. --Chao Mei
        int dcdfd;
#ifdef WIN32
        while ( (dcdfd = _open(dcdname, O_WRONLY|O_BINARY|O_LARGEFILE,
                                _S_IREAD|_S_IWRITE)) < 0)
#else
        while ( (dcdfd = open(dcdname, O_WRONLY|O_LARGEFILE,
                                S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
#endif
        {
                if ( errno != EINTR ) return(DCD_OPENFAILED);
        }

        return(dcdfd);
#else
        //In the case of multiple output files, each slave has its own output file and
        //it needs to be created. --Chao Mei
        return open_dcd_write(dcdname);
#endif
}

pad()

void pad	(	char *	s,
		int	len
	)

Definition at line 105 of file dcdlib.C.

Referenced by write_dcdheader().

{
        int curlen;
        int i;

        curlen=strlen(s);

        if (curlen>len)
        {
                s[len]='\0';
                return;
        }

        for (i=curlen; i<len; i++)
        {
                s[i]=' ';
        }

        s[i]='\0';
}

update_dcdstep_par_header()

int update_dcdstep_par_header

(

int

fd

)

Definition at line 839 of file dcdlib.C.

References LSEEK, NAMD_write, NFILE_POS, NSAVC_POS, NSTEP_POS, OFF_T, and READ.

{
        int32 NSAVC,NSTEP,NFILE;
        /* don't update header until after write succeeds */
        OFF_T end = LSEEK(fd,0,SEEK_CUR);
        LSEEK(fd,NSAVC_POS,SEEK_SET);
        READ(fd,(void*) &NSAVC,sizeof(int32));
        LSEEK(fd,NSTEP_POS,SEEK_SET);
        READ(fd,(void*) &NSTEP,sizeof(int32));
        LSEEK(fd,NFILE_POS,SEEK_SET);
        READ(fd,(void*) &NFILE,sizeof(int32));
        NSTEP += NSAVC;
        NFILE += 1;
        LSEEK(fd,NSTEP_POS,SEEK_SET);
        NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
        LSEEK(fd,NFILE_POS,SEEK_SET);
        NAMD_write(fd,(char*) &NFILE,sizeof(int32));
        LSEEK(fd,end,SEEK_SET);

        return(0);
}

write_dcdheader()

int write_dcdheader	(	int	fd,
		const char *	filename,
		int	N,
		int	NFILE,
		int	NPRIV,
		int	NSAVC,
		int	NSTEP,
		double	DELTA,
		int	with_unitcell
	)

Definition at line 915 of file dcdlib.C.

References NAMD_write, and pad().

Referenced by ComputeQMMgr::recvPartQM(), and Output::recvReplicaDcdData().

{
        int32   out_integer;
        float   out_float;
        char    title_string[200];
        int     user_id;
#ifndef WIN32
        struct  passwd *pwbuf;
#endif
        time_t  cur_time;
        struct  tm *tmbuf;
        char    time_str[11];

        out_integer = 84;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        strcpy(title_string, "CORD");
        NAMD_write(fd, title_string, 4);
        out_integer = NFILE;  /* located at fpos 8 */
        out_integer = 0;  /* ignore the lies */
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = NPRIV;  /* located at fpos 12 */
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = NSAVC;  /* located at fpos 16 */
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = NSTEP;  /* located at fpos 20 */
        out_integer = NPRIV - NSAVC;  /* ignore the lies */
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        out_integer=0;
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        out_float = DELTA;
        NAMD_write(fd, (char *) &out_float, sizeof(float));
  out_integer = with_unitcell ? 1 : 0;
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
  out_integer = 0;
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        out_integer = 24;  // PRETEND TO BE CHARMM24 -JCP
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        out_integer = 84;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));

        out_integer = 164;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = 2;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));

        sprintf(title_string, "REMARKS FILENAME=%s CREATED BY NAMD", filename);
        pad(title_string, 80);
        NAMD_write(fd, title_string, 80);

        char username[100];
#if defined(WIN32) || defined(NO_GETPWUID)
        sprintf(username,"Win32");
#else
        user_id= (int) getuid();
        pwbuf=getpwuid(user_id);
        if ( pwbuf ) sprintf(username,"%s",pwbuf->pw_name);
        else sprintf(username,"%d",user_id);
#endif
        cur_time=time(NULL);
        tmbuf=localtime(&cur_time);
        strftime(time_str, 10, "%m/%d/%y", tmbuf);

        sprintf(title_string, "REMARKS DATE: %s CREATED BY USER: %s",
           time_str, username);
        pad(title_string, 80);
        NAMD_write(fd, title_string, 80);
        out_integer = 164;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = 4;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = N;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));
        out_integer = 4;
        NAMD_write(fd, (char *) & out_integer, sizeof(int32));

        return(0);
}

write_dcdstep()

int write_dcdstep	(	int	fd,
		int	N,
		float *	X,
		float *	Y,
		float *	Z,
		double *	cell
	)

Definition at line 736 of file dcdlib.C.

References LSEEK, NAMD_write, NFILE_POS, NSAVC_POS, NSTEP_POS, OFF_T, READ, X, Y, and Z.

Referenced by ComputeQMMgr::procQMRes(), and Output::recvReplicaDcdData().

{
        int32 NSAVC,NSTEP,NFILE;
        int32 out_integer;

  /* Unit cell */
  if (cell) {
    out_integer = 48;
    NAMD_write(fd, (char *) &out_integer, sizeof(int32));
    NAMD_write(fd, (char *) cell, out_integer);
    NAMD_write(fd, (char *) &out_integer, sizeof(int32));
  }

  /* Coordinates */
  // Note: the value of out_integer wraps for N >= 2^30.
        out_integer = N*4;
  // Use a separate byte count stored without overflow.
  size_t nbytes = ((size_t) N) * 4;

        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) X, nbytes);
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) Y, nbytes);
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        NAMD_write(fd, (char *) Z, nbytes);
        NAMD_write(fd, (char *) &out_integer, sizeof(int32));

        /* don't update header until after write succeeds */
        OFF_T end = LSEEK(fd,0,SEEK_CUR);
        LSEEK(fd,NSAVC_POS,SEEK_SET);
        READ(fd,(void*) &NSAVC,sizeof(int32));
        LSEEK(fd,NSTEP_POS,SEEK_SET);
        READ(fd,(void*) &NSTEP,sizeof(int32));
        LSEEK(fd,NFILE_POS,SEEK_SET);
        READ(fd,(void*) &NFILE,sizeof(int32));
        NSTEP += NSAVC;
        NFILE += 1;
        LSEEK(fd,NSTEP_POS,SEEK_SET);
        NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
        LSEEK(fd,NFILE_POS,SEEK_SET);
        NAMD_write(fd,(char*) &NFILE,sizeof(int32));
        LSEEK(fd,end,SEEK_SET);

        return(0);
}

write_dcdstep_par_cell()

int write_dcdstep_par_cell	(	int	fd,
		double *	cell
	)

Definition at line 785 of file dcdlib.C.

References NAMD_write.

                                                {
        if (cell) {
          int32 out_integer = 48;
          NAMD_write(fd, (char *) &out_integer, sizeof(int32));
          NAMD_write(fd, (char *) cell, out_integer);
          NAMD_write(fd, (char *) &out_integer, sizeof(int32));
        }
        return 0;
}

write_dcdstep_par_slave()

int write_dcdstep_par_slave	(	int	fd,
		int	parL,
		int	parU,
		int	N,
		float *	X,
		float *	Y,
		float *	Z
	)

Definition at line 864 of file dcdlib.C.

References LSEEK, NAMD_write, OFF_T, X, Y, and Z.

                                                                                            {

  /* Coordinates for the N elements handled by this writer */
        int parN = parU-parL+1;
  size_t nbytes = ((size_t)parN) * 4;

        /* x's 1st number of Xs */
        /* skip field for the bytes in X, and the first parL atoms in X*/
        OFF_T xoffset = sizeof(int)+sizeof(float)*((OFF_T)parL);
        LSEEK(fd, xoffset, SEEK_CUR);
        NAMD_write(fd, (char *) X, nbytes);

        /* skip field for the bytes in X and Y; */
        /* skip the remaining atoms in X at number of (N-1)-(parU+1)+1
         * where N-1 is the last atom id, paru+1 is the next atom id. */
        /* skip the first parL atoms in Y; */
        OFF_T yoffset = 2*sizeof(int)+sizeof(float)*((OFF_T)(N-parU+parL-1));
        LSEEK(fd, yoffset, SEEK_CUR);
        NAMD_write(fd, (char *) Y, nbytes);

        OFF_T zoffset = yoffset;
        LSEEK(fd, zoffset, SEEK_CUR);
        NAMD_write(fd, (char *) Z, nbytes);
        return(0);
}

write_dcdstep_par_XYZUnits()

int write_dcdstep_par_XYZUnits	(	int	fd,
		int	N
	)

Definition at line 810 of file dcdlib.C.

References LSEEK, NAMD_write, and OFF_T.

{
  int32 out_integer;

  // number of elements
  // Note: the value of out_integer wraps for N >= 2^30.
  out_integer = N*sizeof(float);

  // For byte seeking, use a properly sized variable.
  OFF_T nbytes = ((OFF_T) N) * sizeof(float);

  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
  // seek to the end of each x y z block and write out the count
  LSEEK(fd, nbytes, SEEK_CUR);
  NAMD_write(fd, (char *) &out_integer, sizeof(int32));

  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
  LSEEK(fd, nbytes, SEEK_CUR);
  NAMD_write(fd, (char *) &out_integer, sizeof(int32));

  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
  LSEEK(fd, nbytes, SEEK_CUR);
  NAMD_write(fd, (char *) &out_integer, sizeof(int32));

  return(0);
}