PLMD::xdrfile Namespace Reference

Classes
struct	t_trnheader
struct	XDR
struct	XDRFILE
	Contents of the abstract XDRFILE data structure. More...

Typedefs
typedef float	matrix[DIM][DIM]
typedef int	mybool
typedef float	rvec[DIM]
typedef struct XDR	XDR
typedef struct XDRFILE	XDRFILE
	Abstract datatype for an portable binary file handle. More...
typedef int(*	xdrproc_t) (XDR *, void *,...)

Enumerations
enum	{   exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,   exdrINT, exdrFLOAT, exdrUINT, exdr3DX,   exdrCLOSE, exdrMAGIC, exdrNOMEM, exdrENDOFFILE,   exdrFILENOTFOUND, exdrNR }
enum	{ FALSE, TRUE }
enum	xdr_op { XDR_ENCODE = 0, XDR_DECODE = 1, XDR_FREE = 2 }

Functions
static int	ctofstr (char *dest, int dest_len, char *src)
	ctofstr (str, len, cstr)
static int	decodebits (int buf[], int num_of_bits)
static void	decodeints (int buf[], int num_of_ints, int num_of_bits, unsigned int sizes[], int nums[])
static int	do_htrn (XDRFILE *xd, mybool bRead, t_trnheader *sh, matrix box, rvec *x, rvec *v, rvec *f)
static int	do_trn (XDRFILE *xd, mybool bRead, int *step, float *t, float *lambda, matrix box, int *natoms, rvec *x, rvec *v, rvec *f)
static int	do_trnheader (XDRFILE *xd, mybool bRead, t_trnheader *sh)
static void	encodebits (int buf[], int num_of_bits, int num)
static void	encodeints (int buf[], int num_of_ints, int num_of_bits, unsigned int sizes[], unsigned int nums[])
void	F77_FUNC (xddcd, XDRDCD)(int *fid
void	F77_FUNC (xdrccd, XDRCCD)(int *fid
void	F77_FUNC (xdrccs, XDRCCS)(int *fid
void	F77_FUNC (xdrclose, XDRCLOSE)(int *fid)
void	F77_FUNC (xdrdcs, XDRDCS)(int *fid
void	F77_FUNC (xdropen, XDROPEN)(int *fid
void	F77_FUNC (xdrrchar, XDRRCHAR)(int *fid
void	F77_FUNC (xdrrdouble, XDRRDOUBLE)(int *fid
void	F77_FUNC (xdrrint, XDRRINT)(int *fid
void	F77_FUNC (xdrropaque, XDRROPAQUE)(int *fid
void	F77_FUNC (xdrrshort, XDRRSHORT)(int *fid
void	F77_FUNC (xdrrsingle, XDRRSINGLE)(int *fid
void	F77_FUNC (xdrrstring, XDRRSTRING)(int *fid
void	F77_FUNC (xdrruchar, XDRRUCHAR)(int *fid
void	F77_FUNC (xdrruint, XDRRUINT)(int *fid
void	F77_FUNC (xdrrushort, XDRRUSHORT)(int *fid
void	F77_FUNC (xdrwchar, XDRWCHAR)(int *fid
void	F77_FUNC (xdrwdouble, XDRWDOUBLE)(int *fid
void	F77_FUNC (xdrwint, XDRWINT)(int *fid
void	F77_FUNC (xdrwopaque, XDRWOPAQUE)(int *fid
void	F77_FUNC (xdrwshort, XDRWSHORT)(int *fid
void	F77_FUNC (xdrwsingle, XDRWSINGLE)(int *fid
void	F77_FUNC (xdrwstring, XDRWSTRING)(int *fid
void	F77_FUNC (xdrwuchar, XDRWUCHAR)(int *fid
void	F77_FUNC (xdrwuint, XDRWUINT)(int *fid
void	F77_FUNC (xdrwushort, XDRWUSHORT)(int *fid
	free (cstr)
static int	ftocstr (char *dest, int dest_len, char *src, int src_len)
	if ((cstr=(char *) malloc((len+1) *sizeof(char)))==NULL)
	if (f77init)
else	if (ftocstr(cfilename, sizeof(cfilename), filename, fn_len))
else	if (ftocstr(cmode, sizeof(cmode), mode, mode_len))
	if (ftocstr(cstr, len+1, str, len))
	if (i==MAX_FORTRAN_XDR)
static int	nFloatSize (t_trnheader *sh, int *nflsz)
int	read_trr (XDRFILE *xd, int natoms, int *step, float *t, float *lambda, matrix box, rvec *x, rvec *v, rvec *f)
int	read_trr_natoms (char *fn, int *natoms)
int	read_xtc (XDRFILE *xd, int natoms, int *step, float *time, matrix box, rvec *x, float *prec)
int	read_xtc_natoms (char *fn, int *natoms)
static int	sizeofint (int size)
static int	sizeofints (int num_of_ints, unsigned int sizes[])
	while (i< MAX_FORTRAN_XDR &&f77xdr[i]!=NULL) i++
int	write_trr (XDRFILE *xd, int natoms, int step, float t, float lambda, matrix box, rvec *x, rvec *v, rvec *f)
int	write_xtc (XDRFILE *xd, int natoms, int step, float time, matrix box, rvec *x, float prec)
static int	xdr_char (XDR *xdrs, char *ip)
static int	xdr_double (XDR *xdrs, double *ip)
static int	xdr_float (XDR *xdrs, float *ip)
static int32_t	xdr_htonl (int32_t x)
static int	xdr_int (XDR *xdrs, int *ip)
static int32_t	xdr_ntohl (int x)
static int	xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
static int	xdr_short (XDR *xdrs, short *ip)
static int	xdr_string (XDR *xdrs, char **ip, unsigned int maxsize)
static int32_t	xdr_swapbytes (int32_t x)
static int	xdr_u_char (XDR *xdrs, unsigned char *ip)
static int	xdr_u_int (XDR *xdrs, unsigned int *ip)
static int	xdr_u_short (XDR *xdrs, unsigned short *ip)
int	xdrfile_close (XDRFILE *xfp)
	Close a previously opened portable binary file, just like fclose() More...
int	xdrfile_compress_coord_double (double *ptr, int ncoord, double precision, XDRFILE *xfp)
	Compress coordiates in a double array to XDR file. More...
int	xdrfile_compress_coord_float (float *ptr, int ncoord, float precision, XDRFILE *xfp)
	Compress coordiates in a float array to XDR file. More...
int	xdrfile_decompress_coord_double (double *ptr, int *ncoord, double *precision, XDRFILE *xfp)
	Decompress coordiates from XDR file to array of doubles. More...
int	xdrfile_decompress_coord_float (float *ptr, int *ncoord, float *precision, XDRFILE *xfp)
	Decompress coordiates from XDR file to array of floats. More...
XDRFILE *	xdrfile_open (const char *path, const char *mode)
	Open a portable binary file, just like fopen() More...
int	xdrfile_read_char (char *ptr, int ndata, XDRFILE *xfp)
	Read one or more char type variable(s) More...
int	xdrfile_read_double (double *ptr, int ndata, XDRFILE *xfp)
	Read one or more double type variable(s) More...
int	xdrfile_read_float (float *ptr, int ndata, XDRFILE *xfp)
	Read one or more float type variable(s) More...
int	xdrfile_read_int (int *ptr, int ndata, XDRFILE *xfp)
	Read one or more integer type variable(s) More...
int	xdrfile_read_opaque (char *ptr, int nbytes, XDRFILE *xfp)
	Read raw bytes from file (unknown datatype) More...
int	xdrfile_read_short (short *ptr, int ndata, XDRFILE *xfp)
	Read one or more short type variable(s) More...
int	xdrfile_read_string (char *ptr, int maxlen, XDRFILE *xfp)
	Read a string (array of characters) More...
int	xdrfile_read_uchar (unsigned char *ptr, int ndata, XDRFILE *xfp)
	Read one or more unsigned char type variable(s) More...
int	xdrfile_read_uint (unsigned int *ptr, int ndata, XDRFILE *xfp)
	Read one or more unsigned integers type variable(s) More...
int	xdrfile_read_ushort (unsigned short *ptr, int ndata, XDRFILE *xfp)
	Read one or more unsigned short type variable(s) More...
int	xdrfile_write_char (char *ptr, int ndata, XDRFILE *xfp)
	Write one or more characters type variable(s) More...
int	xdrfile_write_double (double *ptr, int ndata, XDRFILE *xfp)
	Write one or more double type variable(s) More...
int	xdrfile_write_float (float *ptr, int ndata, XDRFILE *xfp)
	Write one or more float type variable(s) More...
int	xdrfile_write_int (int *ptr, int ndata, XDRFILE *xfp)
	Write one or more integer type variable(s) More...
int	xdrfile_write_opaque (char *ptr, int nbytes, XDRFILE *xfp)
	Write raw bytes to file (unknown datatype) More...
int	xdrfile_write_short (short *ptr, int ndata, XDRFILE *xfp)
	Write one or more short type variable(s) More...
int	xdrfile_write_string (char *ptr, XDRFILE *xfp)
	Write a string (array of characters) More...
int	xdrfile_write_uchar (unsigned char *ptr, int ndata, XDRFILE *xfp)
	Write one or more unsigned characters type variable(s) More...
int	xdrfile_write_uint (unsigned int *ptr, int ndata, XDRFILE *xfp)
	Write one or more unsigned integer type variable(s) More...
int	xdrfile_write_ushort (unsigned short *ptr, int ndata, XDRFILE *xfp)
	Write one or more unsigned short type variable(s) More...
static void	xdrstdio_create (XDR *xdrs, FILE *fp, enum xdr_op xop)
static void	xdrstdio_destroy (XDR *)
static int	xdrstdio_getbytes (XDR *, char *, unsigned int)
static int	xdrstdio_getlong (XDR *, int32_t *)
static unsigned int	xdrstdio_getpos (XDR *)
static int	xdrstdio_putbytes (XDR *, char *, unsigned int)
static int	xdrstdio_putlong (XDR *, int32_t *)
static int	xdrstdio_setpos (XDR *, unsigned int)
static int	xtc_coord (XDRFILE *xd, int *natoms, matrix box, rvec *x, float *prec, mybool bRead)
static int	xtc_header (XDRFILE *xd, int *natoms, int *step, float *time, mybool bRead)

Variables
char	cmode [5]
void int *	data
	else
const char *	exdr_message [exdrNR]
static int	f77init = 1
static XDRFILE *	f77xdr [MAX_FORTRAN_XDR]
*	fid =i
void char *	filename
void char char int	fn_len
int	i =0
void char *	ip
void char int int	len
static const int	magicints []
void char char *	mode
void char char int int	mode_len
void float int *	ncoord
void int int *	ndata
void float int float *	precision
void int int int *	ret
void char *	str
static char	xdr_zero [BYTES_PER_XDR_UNIT] = {0, 0, 0, 0}
static const XDR::xdr_ops	xdrstdio_ops

Typedef Documentation

matrix

typedef float PLMD::xdrfile::matrix[DIM][DIM]

mybool

typedef int PLMD::xdrfile::mybool

rvec

typedef float PLMD::xdrfile::rvec[DIM]

XDR

typedef struct XDR PLMD::xdrfile::XDR

XDRFILE

typedef struct XDRFILE PLMD::xdrfile::XDRFILE

Abstract datatype for an portable binary file handle.

This datatype essentially works just like the standard FILE type in C. The actual contents is hidden in the implementation, so you can only define pointers to it, for use with the xdrfile routines.

If you really need to see the definition it is in xdrfile.c, but you cannot access elements of the structure outside that file.

Warning

The implementation is completely different from the C standard library FILE, so don't even think about using an XDRFILE pointer as an argument to a routine that needs a standard FILE pointer.

xdrproc_t

typedef int(* PLMD::xdrfile::xdrproc_t) (XDR *, void *,...)

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
exdrOK
exdrHEADER
exdrSTRING
exdrDOUBLE
exdrINT
exdrFLOAT
exdrUINT
exdr3DX
exdrCLOSE
exdrMAGIC
exdrNOMEM
exdrENDOFFILE
exdrFILENOTFOUND
exdrNR

anonymous enum

anonymous enum

Enumerator
FALSE
TRUE

xdr_op

enum PLMD::xdrfile::xdr_op

Enumerator
XDR_ENCODE
XDR_DECODE
XDR_FREE

Function Documentation

ctofstr() [1/2]

static int PLMD::xdrfile::ctofstr ( char *  dest, int  dest_len, char *  src  )

static

ctofstr() [2/2]

PLMD::xdrfile::ctofstr	(	str	,
		len	,
		cstr
	)

decodebits()

static int PLMD::xdrfile::decodebits ( int  buf[], int  num_of_bits  )

static

decodeints()

static void PLMD::xdrfile::decodeints ( int  buf[], int  num_of_ints, int  num_of_bits, unsigned int  sizes[], int  nums[]  )

static

do_htrn()

static int PLMD::xdrfile::do_htrn ( XDRFILE *  xd, mybool  bRead, t_trnheader *  sh, matrix  box, rvec *  x, rvec *  v, rvec *  f  )

static

do_trn()

static int PLMD::xdrfile::do_trn ( XDRFILE *  xd, mybool  bRead, int *  step, float *  t, float *  lambda, matrix  box, int *  natoms, rvec *  x, rvec *  v, rvec *  f  )

static

do_trnheader()

static int PLMD::xdrfile::do_trnheader ( XDRFILE *  xd, mybool  bRead, t_trnheader *  sh  )

static

encodebits()

static void PLMD::xdrfile::encodebits ( int  buf[], int  num_of_bits, int  num  )

static

encodeints()

static void PLMD::xdrfile::encodeints ( int  buf[], int  num_of_ints, int  num_of_bits, unsigned int  sizes[], unsigned int  nums[]  )

static

F77_FUNC() [1/26]

void PLMD::xdrfile::F77_FUNC	(	xddcd	,
		XDRDCD
	)

F77_FUNC() [2/26]

void PLMD::xdrfile::F77_FUNC	(	xdrccd	,
		XDRCCD
	)

F77_FUNC() [3/26]

void PLMD::xdrfile::F77_FUNC	(	xdrccs	,
		XDRCCS
	)

F77_FUNC() [4/26]

void PLMD::xdrfile::F77_FUNC	(	xdrclose	,
		XDRCLOSE
	)

F77_FUNC() [5/26]

void PLMD::xdrfile::F77_FUNC	(	xdrdcs	,
		XDRDCS
	)

F77_FUNC() [6/26]

void PLMD::xdrfile::F77_FUNC	(	xdropen	,
		XDROPEN
	)

F77_FUNC() [7/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrchar	,
		XDRRCHAR
	)

F77_FUNC() [8/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrdouble	,
		XDRRDOUBLE
	)

F77_FUNC() [9/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrint	,
		XDRRINT
	)

F77_FUNC() [10/26]

void PLMD::xdrfile::F77_FUNC	(	xdrropaque	,
		XDRROPAQUE
	)

F77_FUNC() [11/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrshort	,
		XDRRSHORT
	)

F77_FUNC() [12/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrsingle	,
		XDRRSINGLE
	)

F77_FUNC() [13/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrstring	,
		XDRRSTRING
	)

F77_FUNC() [14/26]

void PLMD::xdrfile::F77_FUNC	(	xdrruchar	,
		XDRRUCHAR
	)

F77_FUNC() [15/26]

void PLMD::xdrfile::F77_FUNC	(	xdrruint	,
		XDRRUINT
	)

F77_FUNC() [16/26]

void PLMD::xdrfile::F77_FUNC	(	xdrrushort	,
		XDRRUSHORT
	)

F77_FUNC() [17/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwchar	,
		XDRWCHAR
	)

F77_FUNC() [18/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwdouble	,
		XDRWDOUBLE
	)

F77_FUNC() [19/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwint	,
		XDRWINT
	)

F77_FUNC() [20/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwopaque	,
		XDRWOPAQUE
	)

F77_FUNC() [21/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwshort	,
		XDRWSHORT
	)

F77_FUNC() [22/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwsingle	,
		XDRWSINGLE
	)

F77_FUNC() [23/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwstring	,
		XDRWSTRING
	)

F77_FUNC() [24/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwuchar	,
		XDRWUCHAR
	)

F77_FUNC() [25/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwuint	,
		XDRWUINT
	)

F77_FUNC() [26/26]

void PLMD::xdrfile::F77_FUNC	(	xdrwushort	,
		XDRWUSHORT
	)

free()

PLMD::xdrfile::free

(

cstr

)

ftocstr()

static int PLMD::xdrfile::ftocstr ( char *  dest, int  dest_len, char *  src, int  src_len  )

static

if() [1/6]

PLMD::xdrfile::if

(

(cstr=(char *) malloc((len+1) *sizeof(char)))

= =NULL

)

if() [2/6]

PLMD::xdrfile::if

(

f77init

)

if() [3/6]

else PLMD::xdrfile::if

(

ftocstr(cfilename, sizeof(cfilename), filename, fn_len)

)

if() [4/6]

else PLMD::xdrfile::if

(

ftocstr(cmode, sizeof(cmode), mode, mode_len)

)

if() [5/6]

PLMD::xdrfile::if

(

ftocstr(cstr, len+1, str, len)

)

if() [6/6]

PLMD::xdrfile::if

(

i

= =MAX_FORTRAN_XDR

)

nFloatSize()

static int PLMD::xdrfile::nFloatSize ( t_trnheader *  sh, int *  nflsz  )

static

read_trr()

int PLMD::xdrfile::read_trr	(	XDRFILE *	xd,
		int	natoms,
		int *	step,
		float *	t,
		float *	lambda,
		matrix	box,
		rvec *	x,
		rvec *	v,
		rvec *	f
	)

read_trr_natoms()

int PLMD::xdrfile::read_trr_natoms	(	char *	fn,
		int *	natoms
	)

read_xtc()

int PLMD::xdrfile::read_xtc	(	XDRFILE *	xd,
		int	natoms,
		int *	step,
		float *	time,
		matrix	box,
		rvec *	x,
		float *	prec
	)

read_xtc_natoms()

int PLMD::xdrfile::read_xtc_natoms	(	char *	fn,
		int *	natoms
	)

sizeofint()

static int PLMD::xdrfile::sizeofint ( int  size )

static

sizeofints()

static int PLMD::xdrfile::sizeofints ( int  num_of_ints, unsigned int  sizes[]  )

static

while()

PLMD::xdrfile::while

(

)

write_trr()

int PLMD::xdrfile::write_trr	(	XDRFILE *	xd,
		int	natoms,
		int	step,
		float	t,
		float	lambda,
		matrix	box,
		rvec *	x,
		rvec *	v,
		rvec *	f
	)

write_xtc()

int PLMD::xdrfile::write_xtc	(	XDRFILE *	xd,
		int	natoms,
		int	step,
		float	time,
		matrix	box,
		rvec *	x,
		float	prec
	)

xdr_char()

static int PLMD::xdrfile::xdr_char ( XDR *  xdrs, char *  ip  )

static

xdr_double()

static int PLMD::xdrfile::xdr_double ( XDR *  xdrs, double *  ip  )

static

xdr_float()

static int PLMD::xdrfile::xdr_float ( XDR *  xdrs, float *  ip  )

static

xdr_htonl()

static int32_t PLMD::xdrfile::xdr_htonl ( int32_t  x )

static

xdr_int()

static int PLMD::xdrfile::xdr_int ( XDR *  xdrs, int *  ip  )

static

xdr_ntohl()

static int32_t PLMD::xdrfile::xdr_ntohl ( int  x )

static

xdr_opaque()

static int PLMD::xdrfile::xdr_opaque ( XDR *  xdrs, char *  cp, unsigned int  cnt  )

static

xdr_short()

static int PLMD::xdrfile::xdr_short ( XDR *  xdrs, short *  ip  )

static

xdr_string()

static int PLMD::xdrfile::xdr_string ( XDR *  xdrs, char **  ip, unsigned int  maxsize  )

static

xdr_swapbytes()

static int32_t PLMD::xdrfile::xdr_swapbytes ( int32_t  x )

static

xdr_u_char()

static int PLMD::xdrfile::xdr_u_char ( XDR *  xdrs, unsigned char *  ip  )

static

xdr_u_int()

static int PLMD::xdrfile::xdr_u_int ( XDR *  xdrs, unsigned int *  ip  )

static

xdr_u_short()

static int PLMD::xdrfile::xdr_u_short ( XDR *  xdrs, unsigned short *  ip  )

static

xdrfile_close()

int PLMD::xdrfile::xdrfile_close

(

XDRFILE *

xfp

)

Close a previously opened portable binary file, just like fclose()

Use this routine much like calls to the standard library function fopen(). The only difference is that it is used for an XDRFILE handle instead of a FILE handle.

Parameters

xfp	Pointer to an abstract XDRFILE datatype

Returns

0 on success, non-zero on error.

xdrfile_compress_coord_double()

int PLMD::xdrfile::xdrfile_compress_coord_double	(	double *	ptr,
		int	ncoord,
		double	precision,
		XDRFILE *	xfp
	)

Compress coordiates in a double array to XDR file.

This routine will perform lossy compression on the three-dimensional coordinate data data specified and store it in the XDR file. Double will NOT give you any extra precision since the coordinates are compressed. This routine just avoids allocating a temporary array of floats.

The lossy part of the compression consists of multiplying each coordinate with the precision argument and then rounding to integers. We suggest a default value of 1000.0, which means you are guaranteed three decimals of accuracy. The only limitation is that scaled coordinates must still fit in an integer variable, so if the precision is 1000.0 the coordinate magnitudes must be less than +-2e6.

Parameters

ptr	Pointer to coordinates to compress (length 3*ncoord)
ncoord	Number of coordinate triplets in data
precision	Scaling factor for lossy compression. If it is <=0, the default value of 1000.0 is used.
xfp	Handle to portably binary file

Returns

Number of coordinate triplets written. IMPORTANT: Check that this is equal to ncoord - if it is negative, an error occured. This should not happen with normal data, but if your coordinates are NaN or very large (>1e6) it is not possible to use the compression.

Warning

The compression algorithm is not part of the XDR standard, and very complicated, so you will need this xdrfile module to read it later.

xdrfile_compress_coord_float()

int PLMD::xdrfile::xdrfile_compress_coord_float	(	float *	ptr,
		int	ncoord,
		float	precision,
		XDRFILE *	xfp
	)

Compress coordiates in a float array to XDR file.

This routine will perform lossy compression on the three-dimensional coordinate data data specified and store it in the XDR file.

The lossy part of the compression consists of multiplying each coordinate with the precision argument and then rounding to integers. We suggest a default value of 1000.0, which means you are guaranteed three decimals of accuracy. The only limitation is that scaled coordinates must still fit in an integer variable, so if the precision is 1000.0 the coordinate magnitudes must be less than +-2e6.

Parameters

ptr	Pointer to coordinates to compress (length 3*ncoord)
ncoord	Number of coordinate triplets in data
precision	Scaling factor for lossy compression. If it is <=0, the default value of 1000.0 is used.
xfp	Handle to portably binary file

Returns

Number of coordinate triplets written. IMPORTANT: Check that this is equal to ncoord - if it is negative, an error occured. This should not happen with normal data, but if your coordinates are NaN or very large (>1e6) it is not possible to use the compression.

Warning

The compression algorithm is not part of the XDR standard, and very complicated, so you will need this xdrfile module to read it later.

xdrfile_decompress_coord_double()

int PLMD::xdrfile::xdrfile_decompress_coord_double	(	double *	ptr,
		int *	ncoord,
		double *	precision,
		XDRFILE *	xfp
	)

Decompress coordiates from XDR file to array of doubles.

This routine will decompress three-dimensional coordinate data previously stored in an XDR file and store it in the specified array of doubles. Double will NOT give you any extra precision since the coordinates are compressed. This routine just avoids allocating a temporary array of floats.

The precision used during the earlier compression is read from the file and returned - you cannot adjust the accuracy at this stage.

Parameters

ptr	Pointer to coordinates to compress (length>= 3*ncoord)
ncoord	Max number of coordinate triplets to read on input, actual number of coordinate triplets read on return. If this is smaller than the number of coordinates in the frame an error will occur.
precision	The precision used in the previous compression will be written to this variable on return.
xfp	Handle to portably binary file

Returns

Number of coordinate triplets read. If this is negative, an error occured.

Warning

Since we cannot count on being able to set/get the position of large files (>2Gb), it is not possible to recover from errors by re-reading the frame if the storage area you provided was too small. To avoid this from happening, we recommend that you store the number of coordinates triplet as an integer either in a header or just before the compressed coordinate data, so you can read it first and allocated enough memory.

xdrfile_decompress_coord_float()

int PLMD::xdrfile::xdrfile_decompress_coord_float	(	float *	ptr,
		int *	ncoord,
		float *	precision,
		XDRFILE *	xfp
	)

Decompress coordiates from XDR file to array of floats.

This routine will decompress three-dimensional coordinate data previously stored in an XDR file and store it in the specified array of floats.

The precision used during the earlier compression is read from the file and returned - you cannot adjust the accuracy at this stage.

Parameters

ptr	Pointer to coordinates to compress (length>= 3*ncoord)
ncoord	Max number of coordinate triplets to read on input, actual number of coordinate triplets read on return. If this is smaller than the number of coordinates in the frame an error will occur.
precision	The precision used in the previous compression will be written to this variable on return.
xfp	Handle to portably binary file

Returns

Number of coordinate triplets read. If this is negative, an error occured.

Warning

Since we cannot count on being able to set/get the position of large files (>2Gb), it is not possible to recover from errors by re-reading the frame if the storage area you provided was too small. To avoid this from happening, we recommend that you store the number of coordinates triplet as an integer either in a header or just before the compressed coordinate data, so you can read it first and allocated enough memory.

xdrfile_open()

XDRFILE * PLMD::xdrfile::xdrfile_open	(	const char *	path,
		const char *	mode
	)

Open a portable binary file, just like fopen()

Use this routine much like calls to the standard library function fopen(). The only difference is that the returned pointer should only be used with routines defined in this header.

Parameters

path	Full or relative path (including name) of the file
mode	"r" for reading, "w" for writing, "a" for append.

Returns

Pointer to abstract xdr file datatype, or NULL if an error occurs.

xdrfile_read_char()

int PLMD::xdrfile::xdrfile_read_char	(	char *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more char type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of characters to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of characters read

xdrfile_read_double()

int PLMD::xdrfile::xdrfile_read_double	(	double *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more double type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of doubles to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of doubles read

xdrfile_read_float()

int PLMD::xdrfile::xdrfile_read_float	(	float *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more float type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of floats to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of floats read

xdrfile_read_int()

int PLMD::xdrfile::xdrfile_read_int	(	int *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more integer type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of integers to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of integers read

The integer data type is assumed to be less than or equal to 32 bits.

We do not provide any routines for reading/writing 64-bit integers, since

• Not all XDR implementations support it
• Not all machines have 64-bit integers

Split your 64-bit data into two 32-bit integers for portability!

xdrfile_read_opaque()

int PLMD::xdrfile::xdrfile_read_opaque	(	char *	ptr,
		int	nbytes,
		XDRFILE *	xfp
	)

Read raw bytes from file (unknown datatype)

Parameters

ptr	Pointer to memory where data should be written
nbytes	Number of bytes to read. No conversion whatsoever is done.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of bytes read from file

xdrfile_read_short()

int PLMD::xdrfile::xdrfile_read_short	(	short *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more short type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of shorts to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of shorts read

xdrfile_read_string()

int PLMD::xdrfile::xdrfile_read_string	(	char *	ptr,
		int	maxlen,
		XDRFILE *	xfp
	)

Read a string (array of characters)

Parameters

ptr	Pointer to memory where data should be written
maxlen	Maximum length of string. If no end-of-string is encountered, one byte less than this is read and end-of-string appended.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of characters read, including end-of-string

xdrfile_read_uchar()

int PLMD::xdrfile::xdrfile_read_uchar	(	unsigned char *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more unsigned char type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of unsigned characters to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned characters read

xdrfile_read_uint()

int PLMD::xdrfile::xdrfile_read_uint	(	unsigned int *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more unsigned integers type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of unsigned integers to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned integers read

The integer data type is assumed to be less than or equal to 32 bits.

We do not provide any routines for reading/writing 64-bit integers, since

• Not all XDR implementations support it
• Not all machines have 64-bit integers

Split your 64-bit data into two 32-bit integers for portability!

xdrfile_read_ushort()

int PLMD::xdrfile::xdrfile_read_ushort	(	unsigned short *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Read one or more unsigned short type variable(s)

Parameters

ptr	Pointer to memory where data should be written
ndata	Number of unsigned shorts to read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned shorts read

xdrfile_write_char()

int PLMD::xdrfile::xdrfile_write_char	(	char *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more characters type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of characters to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of characters written

xdrfile_write_double()

int PLMD::xdrfile::xdrfile_write_double	(	double *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more double type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of double to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of doubles written

xdrfile_write_float()

int PLMD::xdrfile::xdrfile_write_float	(	float *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more float type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of floats to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of floats written

xdrfile_write_int()

int PLMD::xdrfile::xdrfile_write_int	(	int *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more integer type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of integers to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of integers written

The integer data type is assumed to be less than or equal to 32 bits.

We do not provide any routines for reading/writing 64-bit integers, since

• Not all XDR implementations support it
• Not all machines have 64-bit integers

Split your 64-bit data into two 32-bit integers for portability!

xdrfile_write_opaque()

int PLMD::xdrfile::xdrfile_write_opaque	(	char *	ptr,
		int	nbytes,
		XDRFILE *	xfp
	)

Write raw bytes to file (unknown datatype)

Parameters

ptr	Pointer to memory where data should be read
nbytes	Number of bytes to write. No conversion whatsoever is done.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of bytes written to file

xdrfile_write_short()

int PLMD::xdrfile::xdrfile_write_short	(	short *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more short type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of shorts to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of shorts written

xdrfile_write_string()

int PLMD::xdrfile::xdrfile_write_string	(	char *	ptr,
		XDRFILE *	xfp
	)

Write a string (array of characters)

Parameters

ptr	Pointer to memory where data should be read
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of characters written, including end-of-string

xdrfile_write_uchar()

int PLMD::xdrfile::xdrfile_write_uchar	(	unsigned char *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more unsigned characters type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of unsigned characters to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned characters written

xdrfile_write_uint()

int PLMD::xdrfile::xdrfile_write_uint	(	unsigned int *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more unsigned integer type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of unsigned integers to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned integers written

The integer data type is assumed to be less than or equal to 32 bits.

We do not provide any routines for reading/writing 64-bit integers, since

• Not all XDR implementations support it
• Not all machines have 64-bit integers

Split your 64-bit data into two 32-bit integers for portability!

xdrfile_write_ushort()

int PLMD::xdrfile::xdrfile_write_ushort	(	unsigned short *	ptr,
		int	ndata,
		XDRFILE *	xfp
	)

Write one or more unsigned short type variable(s)

Parameters

ptr	Pointer to memory where data should be read
ndata	Number of unsigned shorts to write.
xfp	Handle to portable binary file, created with xdrfile_open()

Returns

Number of unsigned shorts written

xdrstdio_create()

static void PLMD::xdrfile::xdrstdio_create ( XDR *  xdrs, FILE *  fp, enum xdr_op  xop  )

static

xdrstdio_destroy()

static void PLMD::xdrfile::xdrstdio_destroy ( XDR *  xdrs )

static

xdrstdio_getbytes()

static int PLMD::xdrfile::xdrstdio_getbytes ( XDR *  xdrs, char *  addr, unsigned int  len  )

static

xdrstdio_getlong()

static int PLMD::xdrfile::xdrstdio_getlong ( XDR *  xdrs, int32_t *  lp  )

static

xdrstdio_getpos()

static unsigned int PLMD::xdrfile::xdrstdio_getpos ( XDR *  xdrs )

static

xdrstdio_putbytes()

static int PLMD::xdrfile::xdrstdio_putbytes ( XDR *  xdrs, char *  addr, unsigned int  len  )

static

xdrstdio_putlong()

static int PLMD::xdrfile::xdrstdio_putlong ( XDR *  xdrs, int32_t *  lp  )

static

xdrstdio_setpos()

static int PLMD::xdrfile::xdrstdio_setpos ( XDR *  xdrs, unsigned int  pos  )

static

xtc_coord()

static int PLMD::xdrfile::xtc_coord ( XDRFILE *  xd, int *  natoms, matrix  box, rvec *  x, float *  prec, mybool  bRead  )

static

xtc_header()

static int PLMD::xdrfile::xtc_header ( XDRFILE *  xd, int *  natoms, int *  step, float *  time, mybool  bRead  )

static

Variable Documentation

cmode

char PLMD::xdrfile::cmode[5]

data

void double * PLMD::xdrfile::data

else

PLMD::xdrfile::else

Initial value:

{
                f77xdr[i]=xdrfile_open(cfilename,cmode)

exdr_message

const char * PLMD::xdrfile::exdr_message

Initial value:

= {
        "OK", 
        "Header",
        "String", 
        "Double",
        "Integer",
        "Float",
        "Unsigned integer",
        "Compressed 3D coordinate",
        "Closing file",
        "Magic number",
        "Not enough memory",
        "End of file",
        "File not found" 
}

f77init

int PLMD::xdrfile::f77init = 1

static

f77xdr

XDRFILE* PLMD::xdrfile::f77xdr[MAX_FORTRAN_XDR]

static

fid

* PLMD::xdrfile::fid =i

filename

void char* PLMD::xdrfile::filename

fn_len

void char char int PLMD::xdrfile::fn_len

i

PLMD::xdrfile::i =0

ip

void unsigned short * PLMD::xdrfile::ip

len

void char int int PLMD::xdrfile::len

Initial value:

{
        char *cstr

magicints

const int PLMD::xdrfile::magicints[]

static

Initial value:

= 
{
    0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
    80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,
    1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003, 
    16384, 20642, 26007, 32768, 41285, 52015, 65536,82570, 104031, 
    131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561, 
    832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 
    4194304, 5284491, 6658042, 8388607, 10568983, 13316085, 16777216 
}

mode

void char char* PLMD::xdrfile::mode

mode_len

void char char int int PLMD::xdrfile::mode_len

Initial value:

{
        char cfilename[512]

ncoord

void double int * PLMD::xdrfile::ncoord

ndata

void char int * PLMD::xdrfile::ndata

precision

void double int double * PLMD::xdrfile::precision

ret

void double int double int * PLMD::xdrfile::ret

Initial value:

{
        *ret = xdrfile_read_int(data,*ndata,f77xdr[*fid])

str

void char * PLMD::xdrfile::str

xdr_zero

char PLMD::xdrfile::xdr_zero[BYTES_PER_XDR_UNIT] = {0, 0, 0, 0}

static

xdrstdio_ops

const XDR::xdr_ops PLMD::xdrfile::xdrstdio_ops

static

Initial value:

=
        {
                xdrstdio_getlong,               
                xdrstdio_putlong,               
                xdrstdio_getbytes,              
                xdrstdio_putbytes,      
                xdrstdio_getpos,                
                xdrstdio_setpos,                
                xdrstdio_destroy,               
        }